RetrogeneDB ID: | retro_mmus_1339 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 15:38990233..38992007(+) | ||
| Located in intron of: | ENSMUSG00000097875 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Atad3a | ||
| Ensembl ID: | ENSMUSG00000029036 | ||
| Aliases: | Atad3a, 2400004H09Rik, Atad3, Tob3, mKIAA1273 | ||
| Description: | ATPase family, AAA domain containing 3A [Source:MGI Symbol;Acc:MGI:1919214] |
Retrocopy-Parental alignment summary:
>retro_mmus_1339
ATGTCGTGGCTCTTCGGCATCAAGGGTCCTAAGGGCGAAGGCACAGGGCCTCCGCTGCCCTTGCCGCCCGCTCAACCTGG
GGCGGAGGGCGGCGGTGACCGCGGTGCGGGAGACCGGCCATCGCCCAAGGACAAATGGAGCAACTTCGACCCGACGGGCC
TGGAACGTGCGGCCAAAGTGGCGCGCGAGTTGGAGCACTCGCGCCATGCCAAGGAGGCACGGAGTCTTGCACAGATGCAG
GAGCAGACACTGCAGCTGGAACAACAGTCCAAGCTCAAGGAGTACGAAGCTGCCGTAGAGCAGCTGAAGAGTGAACAGAT
CCGTGTGCAAGCCGAGGAAAGAAGGAAAACCCTGACTGAAGAGACACGACAGCACCAGGCTAGGGCCCAGTACCAGGATA
AGCTAGCTCGACAACGCTATGAGGACCAGCTGAAACAACAGCAACTTCTGAATGGAGAGAATTTAAGGAAACAAGAGGAG
TCTGTGCAGAAACAGGAGGCCATACGGCGAGCCACTGTGGAGCGCGAGATGGAGCTGCGGCATAAAAAACGAGATGTTGC
GGGTGGAAGCTGAAGCCGGAGCACGGGTCAAGGCTGATCAAGAGAATGCAGATATCATCCGGGAACAGATTTGACTCAAG
GCTGCTGAGCACCTCCAGACAATCTTGGAGTCTATCAGGACAGCTGGAACCTTGTTTGGTGAAGGATTCCGTGCCTTTGT
GACAGACTGGGACAAAGTGACAGCTACGGTGGCTGGGTTGACACTATTAGCTGTTGGAGTCTATTCTGCCAAGAATGCTA
CCTCTGTTGCTGGTCGGTATATTGAGGCCCGATTGGGAAAGCCGTCCTTGGTGAGAGAGACCTCCCGAATCTCAGTGCTA
GAGGCATTGAGGCATCCCATCCAGGTCAGCAGGCGACTGGTCAGCAGACCCCAGGATGCATTGGAGGGCGTCATCCTCAG
TCCTAGCCTGGAGGCACGGGTACGAAATATTGCCATCGCAACAAGAAATACCAAGAAGAACAAAAGCCTGTATAGAAACG
TCCTGATGTATGGGCCCCCGGGGACTGGCAAGACACTATTTTCCAAGAAACTTGCACTGCATTCAGGCATGGACTACGCC
ATCATGACAGGCGGGGACGTGGCCCCAATGGGGAGGGAGGGTGTGACTGCCGTGCACGAGGTCTTTGAATGGGCAAGCAC
CAACCGACGAGGCCTCCTGCTCTTTGTGGATGAAGCAGATGCCTTCCTCAGGAAACGAGCGACTGAAAAGATAAGTGAAG
AGCTCAGGGCTACTCTGAATGAATTCCTACATAGGACAGGACAACACAGTAGTAAGTTCATGCTGGTTGTGGCCAGTAAC
CAGCCTGAGCAGTTTGATTGGGCTATCAATGACCGCGTTGACGAGATGGTCTGCTTTGCCCTGCCATAGCGGGAGGAGCG
AGAGCACCTGGTGAGAATGTATTTTGACAAGTATGTCCTTAAGCCGGCCACAGAAGGAAAGCAATGCTTGAAGGTGGCCC
AGTTTGACCACGGAAAGAAATGCTAGGAGGTCGCCCAGCTGAAGGAGGGGATGTCAGGCCGGGAGATTGCTCAGCTTGCT
GTGGTGTGGCAGGCCATAGCATATTCATCTGAGGACGGAGTCCTCACGGAGGCTATGATGGATGCCCGTGTGCAGGATGC
TGTGCAGCAGCACCAGCAGAAGATGCAGTGGCTTAAAGTAGTGAGACCCGATTCCCAGACCAACAAGCCGCCACATCCTT
CACTCCTCAGCTGT
ORF - retro_mmus_1339 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.1 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSWLFGIKGPKGEGTGPPLPLPPAQPGAEGGGDRGAGDRPSPKDKWSNFDPTGLERAAKAARELEHSRHA |
| MSWLFGIKGPKGEGTGPPLPLPPAQPGAEGGGDRGAGDRPSPKDKWSNFDPTGLERAAK.ARELEHSRHA | |
| Retrocopy | MSWLFGIKGPKGEGTGPPLPLPPAQPGAEGGGDRGAGDRPSPKDKWSNFDPTGLERAAKVARELEHSRHA |
| Parental | KEALSLAQMQEQTLQLEQQSKLKEYEAAVEQLKSEQIRVQAEERRKTLTEETRQHQARAQYQDKLARQRY |
| KEA.SLAQMQEQTLQLEQQSKLKEYEAAVEQLKSEQIRVQAEERRKTLTEETRQHQARAQYQDKLARQRY | |
| Retrocopy | KEARSLAQMQEQTLQLEQQSKLKEYEAAVEQLKSEQIRVQAEERRKTLTEETRQHQARAQYQDKLARQRY |
| Parental | EDQLKQQQLLNEENLRKQEESVQKQEAIRRATVEREMELRHK-NEMLRVEAEARARAKADRENADIIREQ |
| EDQLKQQQLLN.ENLRKQEESVQKQEAIRRATVEREMELRHK.NEMLRVEAEA.AR.KAD.ENADIIREQ | |
| Retrocopy | EDQLKQQQLLNGENLRKQEESVQKQEAIRRATVEREMELRHK>NEMLRVEAEAGARVKADQENADIIREQ |
| Parental | IRLKAAEHRQTILESIRTAGTLLGEGFRAFVTDWDKVTATVAGLTLLAVGVYSAKNATSVAGRYIEARLG |
| I.LKAAEH.QTILESIRTAGTL.GEGFRAFVTDWDKVTATVAGLTLLAVGVYSAKNATSVAGRYIEARLG | |
| Retrocopy | I*LKAAEHLQTILESIRTAGTLFGEGFRAFVTDWDKVTATVAGLTLLAVGVYSAKNATSVAGRYIEARLG |
| Parental | KPSLVRETSRISVLEALRHPIQVSRRLVSRPQDALEGVILSPSLEARVRDIAIATRNTKKNKSLYRNVLM |
| KPSLVRETSRISVLEALRHPIQVSRRLVSRPQDALEGVILSPSLEARVR.IAIATRNTKKNKSLYRNVLM | |
| Retrocopy | KPSLVRETSRISVLEALRHPIQVSRRLVSRPQDALEGVILSPSLEARVRNIAIATRNTKKNKSLYRNVLM |
| Parental | YGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAPMGREGVTAMHKVFDWASTSRRGLLLFVDEADAFLRKR |
| YGPPGTGKTLF.KKLALHSGMDYAIMTGGDVAPMGREGVTA.H.VF.WAST.RRGLLLFVDEADAFLRKR | |
| Retrocopy | YGPPGTGKTLFSKKLALHSGMDYAIMTGGDVAPMGREGVTAVHEVFEWASTNRRGLLLFVDEADAFLRKR |
| Parental | ATEKISEDLRATLNAFLHRTGQHSSKFMLVLASNQPEQFDWAINDRIDEMVCFALPQREERERLVRMYFD |
| ATEKISE.LRATLN.FLHRTGQHSSKFMLV.ASNQPEQFDWAINDR.DEMVCFALP.REERE.LVRMYFD | |
| Retrocopy | ATEKISEELRATLNEFLHRTGQHSSKFMLVVASNQPEQFDWAINDRVDEMVCFALP*REEREHLVRMYFD |
| Parental | KYVLKPATEGKQRLKVAQFDYGKKCSEVAQLTEGMSGREIAQLAVAWQAMAYSSEDGVLTEAMMDARVQD |
| KYVLKPATEGKQ.LKVAQFD.GKKC.EVAQL.EGMSGREIAQLAV.WQA.AYSSEDGVLTEAMMDARVQD | |
| Retrocopy | KYVLKPATEGKQCLKVAQFDHGKKC*EVAQLKEGMSGREIAQLAVVWQAIAYSSEDGVLTEAMMDARVQD |
| Parental | AVQQHQQKMQWLKVERPDSQTNKPPHPSLLSC |
| AVQQHQQKMQWLKV.RPDSQTNKPPHPSLLSC | |
| Retrocopy | AVQQHQQKMQWLKVVRPDSQTNKPPHPSLLSC |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain | 0 .02 RPM | 30 .68 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 47 .16 RPM |
| SRP007412_heart | 0 .12 RPM | 53 .33 RPM |
| SRP007412_kidney | 0 .17 RPM | 69 .49 RPM |
| SRP007412_liver | 0 .03 RPM | 65 .68 RPM |
| SRP007412_testis | 0 .23 RPM | 14 .18 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1339 was not detected
No EST(s) were mapped for retro_mmus_1339 retrocopy.
No TSS is located nearby retro_mmus_1339 retrocopy 5' end.
retro_mmus_1339 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1339 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000029036 | 1 retrocopy |
retro_mmus_1339 ,
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