RetrogeneDB ID: | retro_mmus_227 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:128644912..128646391(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000037827 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Tom1 | ||
| Ensembl ID: | ENSMUSG00000042870 | ||
| Aliases: | None | ||
| Description: | target of myb1 homolog (chicken) [Source:MGI Symbol;Acc:MGI:1338026] |
Retrocopy-Parental alignment summary:
>retro_mmus_227
ATGGACTTTCTCCTGGGAAATCCGTTCAGCTCTCCGGTGGGACAACGGATCGAGAAAGCTACAGATGGCTCCCTGCAGAG
CGAGGACTGGGCCCTCAACATGGAAATCTGTGACATCATCAACGAGACGGAGGAAGGCCCCAAAGATGCCTTCCGAGCAG
TGAAGAAGCGAATTATGGGGAATAAGAATTTCCATGAGGTCATGCTGGCCCTTACGGTCTTGGAAACATGTGTTAAGAAC
TGTGGGCACCGCTTCCATGTACTGGTGGCCAACCAGGACTTTGTAGAGAATGTGCTGGTGAGGACCATCCTGCCGAAGAA
CAATCCACCCACCATTGTGCATGACAAGGTGTTGAACCTCATCCAGTCCTGGGCTGACGCGTTCCGCAGCTCACCTGATT
TGACAGGTGTTGTTGCTGTCTACGAGGACCTGCGAAGGAAGGGCCTAGAATTTCCCATGACTGACCTGGACATGCTGTCG
CCCATCCACACACCCCAGAGAACTGTATTCAACTCAGAGACACCATCCAGACAGAACTCTGTGAGTTCCAACACCAGTCA
GCGTGGAGACCTGAGCCAGCATGCCACCCCTCTGCCCACTCCAGCTGTTCTCCCGGGTGACTCACCCATCACACCGACTC
CTGAGCAGATTGGGAAGCTGCGCAGTGAGCTGGAGATGGTGAGCGGAAACGTGCGAGTGATGTCAGAGATGCTGACAGAG
CTGGTGCCCACCCAGGTAGAGCCTGCAGACCTGGAGCTACTACAGGAACTGAACCGCACCTGCCGTGCCATGCAGCAGCG
GATCCTGGAGCTTATCCCACGCATCTCCAATGAGCAGCTGACGGAGGAGCTGCTCATGATCAACGACAACCTCAACAACG
TGTTTCTGCGCCATGAACGGTTTGAACGCTTCCGAACAGGCCAGACTGCTAAGGCCTCCAGTGAAGCTGAGCTAGCTACT
GACCTGATTGACATGGGTCCTGACCCCGCAGCCACAAACAACCTCTCATCTCAACTGGCAGGAATGAACCTTGGCTCCAG
AAGTGTGAGAGCTGGCCTGCAGTCTCTGGAGACCTCAGGTCACCTGGAAGATGACTTTGACATGTTTGCTCTGACTCGGG
GCAGCTCACTGGCTGACCAACGGAAAGGGGTCAAATATGAAGCTCCCCAAACCACAGATGGCCTGGCTGGGGCCCTAGAT
GCCCGGCAGCAGAGCACCGGAGCGATCCCAGCCACTCAGGCCCGCATCATGGAGGACATTGAGCAGTGGCTGTCCACAGA
TGTGGGGAACAGTGCTGAGGAGCCCTCTGGTGTCACCAGTGAAGAATTTGACAAATTTCTGGAAGAACGAGCCAAAGCTG
CTGATCGACTTCCCAACCTGGCCAGCCCTTCAGCCGAGGGACCCCCCAGACCATCTCCTGGAACAGCCCCTCGGAGGAAG
ACCCAGGAGAAGGACGATGACATGCTGTTTGCCTTATGA
ORF - retro_mmus_227 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDAFRAVKKRIMGNKNFHEVMLA |
| MDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDAFRAVKKRIMGNKNFHEVMLA | |
| Retrocopy | MDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDAFRAVKKRIMGNKNFHEVMLA |
| Parental | LTVLETCVKNCGHRFHVLVANQDFVENVLVRTILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVAV |
| LTVLETCVKNCGHRFHVLVANQDFVENVLVRTILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVAV | |
| Retrocopy | LTVLETCVKNCGHRFHVLVANQDFVENVLVRTILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVAV |
| Parental | YEDLRRKGLEFPMTDLDMLSPIHTPQRTVFNSETPSRQNSVSSNTSQRGDLSQHATPLPTPAVLPGDSPI |
| YEDLRRKGLEFPMTDLDMLSPIHTPQRTVFNSETPSRQNSVSSNTSQRGDLSQHATPLPTPAVLPGDSPI | |
| Retrocopy | YEDLRRKGLEFPMTDLDMLSPIHTPQRTVFNSETPSRQNSVSSNTSQRGDLSQHATPLPTPAVLPGDSPI |
| Parental | TPTPEQIGKLRSELEMVSGNVRVMSEMLTELVPTQVEPADLELLQELNRTCRAMQQRILELIPRISNEQL |
| TPTPEQIGKLRSELEMVSGNVRVMSEMLTELVPTQVEPADLELLQELNRTCRAMQQRILELIPRISNEQL | |
| Retrocopy | TPTPEQIGKLRSELEMVSGNVRVMSEMLTELVPTQVEPADLELLQELNRTCRAMQQRILELIPRISNEQL |
| Parental | TEELLMINDNLNNVFLRHERFERFRTGQTAKASSEAELATDLIDMGPDPAATNNLSSQLAGMNLGSRSVR |
| TEELLMINDNLNNVFLRHERFERFRTGQTAKASSEAELATDLIDMGPDPAATNNLSSQLAGMNLGSRSVR | |
| Retrocopy | TEELLMINDNLNNVFLRHERFERFRTGQTAKASSEAELATDLIDMGPDPAATNNLSSQLAGMNLGSRSVR |
| Parental | AGLQSLETSGHLEDDFDMFALTRGSSLADQRKGVKYEAPQTTDGLAGALDARQQSTGAIPATQARIMEDI |
| AGLQSLETSGHLEDDFDMFALTRGSSLADQRKGVKYEAPQTTDGLAGALDARQQSTGAIPATQARIMEDI | |
| Retrocopy | AGLQSLETSGHLEDDFDMFALTRGSSLADQRKGVKYEAPQTTDGLAGALDARQQSTGAIPATQARIMEDI |
| Parental | EQWLSTDVGNSAEEPSGVTSEEFDKFLEERAKAADRLPNLASPSAEGPPRPSPGTAPRRKTQEKDDDMLF |
| EQWLSTDVGNSAEEPSGVTSEEFDKFLEERAKAADRLPNLASPSAEGPPRPSPGTAPRRKTQEKDDDMLF | |
| Retrocopy | EQWLSTDVGNSAEEPSGVTSEEFDKFLEERAKAADRLPNLASPSAEGPPRPSPGTAPRRKTQEKDDDMLF |
| Parental | AL |
| AL | |
| Retrocopy | AL |
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 .07 RPM | 4 .11 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 4 .08 RPM |
| SRP007412_heart | 0 .44 RPM | 10 .30 RPM |
| SRP007412_kidney | 0 .19 RPM | 6 .60 RPM |
| SRP007412_liver | 0 .16 RPM | 3 .66 RPM |
| SRP007412_testis | 0 .18 RPM | 10 .20 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_227 was not detected
73 EST(s) were mapped to retro_mmus_227 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| AA388933 | 128644887 | 128645433 | 99.9 | 544 | 0 | 541 |
| AA463074 | 128644857 | 128645303 | 99.6 | 444 | 2 | 442 |
| AA592451 | 128644867 | 128645486 | 100 | 467 | 0 | 464 |
| AA656929 | 128644889 | 128645445 | 99.8 | 389 | 0 | 385 |
| AI664521 | 128644884 | 128645476 | 99.5 | 587 | 2 | 583 |
| AW457392 | 128644857 | 128645227 | 100 | 370 | 0 | 370 |
| BB656379 | 128644841 | 128645403 | 99 | 554 | 5 | 546 |
| BB855166 | 128644873 | 128645349 | 99.8 | 475 | 1 | 474 |
| BB855766 | 128644899 | 128645392 | 100 | 493 | 0 | 493 |
| BE290228 | 128644917 | 128645532 | 98.9 | 607 | 7 | 599 |
| BE849518 | 128644874 | 128645571 | 99.5 | 381 | 2 | 378 |
| BE948382 | 128644857 | 128645227 | 100 | 370 | 0 | 370 |
| BF469415 | 128645021 | 128645440 | 100 | 419 | 0 | 419 |
| BF582751 | 128644871 | 128645538 | 99.4 | 656 | 3 | 644 |
| BG082477 | 128644897 | 128645461 | 100 | 564 | 0 | 564 |
| BG796721 | 128645119 | 128645564 | 98.7 | 426 | 6 | 415 |
| BI452669 | 128644850 | 128645559 | 99.3 | 703 | 5 | 697 |
| BI693400 | 128645041 | 128645742 | 100 | 700 | 0 | 699 |
| BI872084 | 128644918 | 128645729 | 99.7 | 802 | 2 | 792 |
| BM935331 | 128644858 | 128645223 | 100 | 365 | 0 | 365 |
| BQ258180 | 128644890 | 128645555 | 100 | 665 | 0 | 665 |
| BQ266756 | 128644893 | 128645408 | 100 | 515 | 0 | 515 |
| BX526426 | 128644883 | 128645406 | 100 | 523 | 0 | 523 |
| BY000536 | 128644884 | 128645296 | 99 | 393 | 4 | 388 |
| BY020933 | 128644863 | 128645237 | 99.2 | 371 | 3 | 368 |
| BY077578 | 128644869 | 128645241 | 100 | 372 | 0 | 372 |
| BY080384 | 128644841 | 128645210 | 100 | 368 | 0 | 368 |
| BY082888 | 128644860 | 128645236 | 99.3 | 373 | 3 | 370 |
| BY084957 | 128644842 | 128645201 | 100 | 359 | 0 | 359 |
| BY087901 | 128644860 | 128645239 | 100 | 379 | 0 | 379 |
| BY114739 | 128644876 | 128645208 | 100 | 332 | 0 | 332 |
| BY114752 | 128644876 | 128645193 | 100 | 317 | 0 | 317 |
| BY122432 | 128644860 | 128645163 | 100 | 303 | 0 | 303 |
| BY133290 | 128644876 | 128645240 | 99.8 | 363 | 1 | 362 |
| BY172224 | 128644860 | 128645217 | 98.1 | 350 | 7 | 343 |
| BY229804 | 128644841 | 128645215 | 99.8 | 373 | 1 | 372 |
| BY240445 | 128644860 | 128645392 | 99.4 | 449 | 3 | 445 |
| BY256016 | 128644863 | 128645622 | 100 | 445 | 0 | 444 |
| BY256900 | 128644884 | 128645433 | 96.6 | 450 | 14 | 431 |
| BY256915 | 128644884 | 128645438 | 99.2 | 466 | 4 | 461 |
| BY257524 | 128644884 | 128645429 | 99.2 | 460 | 4 | 455 |
| BY261427 | 128644876 | 128645327 | 99.6 | 448 | 2 | 446 |
| BY267376 | 128644846 | 128645234 | 100 | 388 | 0 | 388 |
| BY270637 | 128644846 | 128645276 | 100 | 430 | 0 | 430 |
| BY272523 | 128644876 | 128645309 | 100 | 433 | 0 | 433 |
| BY281327 | 128644841 | 128645271 | 99.8 | 429 | 1 | 428 |
| BY316054 | 128644841 | 128645217 | 99.5 | 374 | 2 | 372 |
| BY320119 | 128644841 | 128645213 | 100 | 372 | 0 | 372 |
| BY346472 | 128644876 | 128645188 | 99.7 | 310 | 1 | 309 |
| BY779510 | 128644860 | 128645295 | 97.2 | 349 | 7 | 338 |
| BY782058 | 128644860 | 128645270 | 99.4 | 329 | 2 | 326 |
| BY789663 | 128644860 | 128645277 | 99.8 | 337 | 1 | 335 |
| CA531936 | 128644991 | 128645502 | 99.9 | 510 | 1 | 509 |
| CA533933 | 128644843 | 128645660 | 100 | 503 | 0 | 502 |
| CA542181 | 128644895 | 128645389 | 99.6 | 492 | 2 | 490 |
| CA548913 | 128644897 | 128645318 | 99.8 | 420 | 1 | 419 |
| CA549695 | 128644897 | 128645412 | 100 | 515 | 0 | 515 |
| CA554147 | 128644897 | 128645412 | 100 | 515 | 0 | 515 |
| CA562541 | 128644885 | 128645321 | 100 | 436 | 0 | 436 |
| CF153923 | 128644897 | 128645433 | 100 | 536 | 0 | 536 |
| CF900161 | 128644854 | 128645544 | 100 | 690 | 0 | 690 |
| CJ067650 | 128644863 | 128645335 | 99.8 | 471 | 1 | 470 |
| CJ067786 | 128644863 | 128645320 | 99.6 | 455 | 2 | 453 |
| CJ134695 | 128644876 | 128645503 | 100 | 626 | 0 | 625 |
| CJ134877 | 128644876 | 128645507 | 100 | 630 | 0 | 629 |
| CJ139478 | 128644860 | 128645348 | 100 | 488 | 0 | 488 |
| CJ162451 | 128644869 | 128645328 | 100 | 459 | 0 | 459 |
| CJ164904 | 128644876 | 128645301 | 100 | 407 | 0 | 406 |
| CJ184744 | 128644876 | 128645297 | 100 | 403 | 0 | 402 |
| CK333620 | 128644897 | 128645302 | 99.8 | 404 | 1 | 403 |
| CN684810 | 128645088 | 128645738 | 99.9 | 649 | 1 | 648 |
| CX230135 | 128645090 | 128645412 | 98.5 | 314 | 5 | 306 |
| DN176210 | 128644901 | 128645226 | 99.7 | 324 | 1 | 323 |
No TSS is located nearby retro_mmus_227 retrocopy 5' end.
retro_mmus_227 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_227 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 | ENSMUSG00000042870 | 1 retrocopy |
retro_mmus_227 ,
|