Supplementary table. RefSeq transcripts beginning within a TEa
Gene / Probable TE involvement in humanb / TE in mousec / Human expressiond / Mouse expressioneCYP19 / LTR is one of at least six promoters (primer extension [1]; promoter constructs [2]; review [3]) / No / LTR drives very high placental expression (transgenic mice [4]) / No placental expression [3]
TMPRSS3 / LTR and Aluf as an alternative promoter (5 RACE [5]) / No / TE form expressed primarily in PBLs;
other forms are widespread (RT-PCR [5]) / Inner ear, kidney, stomach, testis (RT-PCR [6])
HYAL-4 / Antisense L1 and Alufas only known promoter (5 RACE [7]) / No / Primarily placenta (northern [7]) / Primarily skin (1 cDNA , seven ESTs [8])
ENTPD1 (CD39) / LTR as one of two promoters and results in HERV-derived N-terminus (5 RACE [9]) / No / LTR drives expression in placenta (two cDNAs and one EST [8]) and melanoma (two ESTs [8]); overall expression widespread (northern [10,11]) / Widespread (northern [12]; three cDNAs [8])
CASPR4 / LTR one of three promoters and results in HERV-derived N-terminus / No / LTR form expressed in brain, testis, tumors (one cDNA for each [8]); overall expression high in brain and spinal cord (northern [13]; 3 cDNAs [8]). / Brain (northern [13])
MKKS / LTR and L2f as an alternative promoter (5 RACE [14]) / No / TE form in testis (one EST) and fetal tissues (5 RACE [14]); overall expression widespread (northern [14]) / Widespread (northern [14])
CA1 / LTR one of two major promoters (S1 mapping, primer extension, promoter constructs [15]) / Yes / LTR drives erythroid expression (primer extension [15,16]) / LTR drives erythroid expression
[17]
SPAM1
(PH20) / Antisense ERV as only known promoter / Yes / Primarily testis (northern [7]; two cDNAs [8]) / Primarily testis (northern [18])
KLK11 / MIR one of three promoters and leads to alternative N-terminus (5 RACE [19]) / Yes / Widespread (northern [19]; RT-PCR [20]) / Brain and prostate (northern [21])
MSLN
(MPF) / LTR as one of two promoters and part of 5 UTR of other transcript form; alternative promoter is an MIR (promoter constructs [22]) / Yes for both / Widespread (northern [23,24]) / Widespread but not from LTR or MIR (northern [25]; ~10 cDNAs and ESTs [8])
BAAT / LTR as the only known promoter / No / Liver (three cDNAs [8]) / Liver (northern [26])
MAD1L1 / LTR as one of two promoters and part of 5 UTR of other form (5 RACE [27]) / No / LTR form in tumors (~10 cDNAs and ESTs [8]); other form widespread (northern [27]) / Widespread [8]
CLDN14 / LTR as one of two promoters / No / LTR form in melanoma and skin (one cDNA [8] and kidney (northern, [28]); other form in liver (northern, [28]) / Widespread [29]
SIAT1 / ERV as one of at least three promoters / No / ERV form in mature B cells (northern [30]); other forms in various tissues (northern [30,31]) / B-cell and liver expression from multiple promoters (Northern [32])
FUT5 / Antisense Alu and L1f as only known promoter (5’ RACE [33]) / NA / Low expression in colon, liver; much lower expression compared with related FUTs that use other promoters (RT-PCR [33]) / FUTs expanded after human–mouse split so no mouse ortholog
ILT2 (LIR1, LILRB1) / ERV as alternative promoter / NA / Only ILT known to be expressed in natural killer cells [34] / ILTs expanded after human –mouse split
aAbbreviations: Alu, Alu repeat sequences; ERV, endogenous retrovirus-like element; LTR, long terminal repeat; L1 and L2, long interspersed nuclear element family members; MIR, mammalian interspersed element; NA, not applicable; TE, transposable element.
bAs predicted from Genome Browser annotation, databases or literature. TE promoters are depicted in bold if specifically analyzed in literature by promoter assays or 5’ RACE (rapid amplification of cDNA ends). Evidence for the TE as promoter is indicated in parentheses with references.
cPresence of TE in mouse was determined by Genome Browser annotation, BLAST and dot plot alignments.
dInformation from literature, where available, or expression databases. Expression pattern of the TE-initiated form is given if known. The type of evidence and references are given in parentheses.
eInformation from literature or databases with attention to patterns that differ from human.
fThe apparent promoter region is composed of sections of two different TEs.
References
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