RetrogeneDB ID: | retro_btau_1451 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 6:35008570..35010337(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000045523 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FARSB | ||
| Ensembl ID: | ENSBTAG00000011649 | ||
| Aliases: | None | ||
| Description: | phenylalanyl-tRNA synthetase beta chain [Source:RefSeq peptide;Acc:NP_001098491] |
Retrocopy-Parental alignment summary:
>retro_btau_1451
ATGCCGACTGTCAGCGTGAAGTGAGATCTGCTCTTCCGAGCCCTGGGCCGGACCTACACTGATGAAGAATTTGATGAACT
GTGCTTTGAATTTGGACTGGAACTTGATGAAATTACATCTGAAAAGGAAATTATAAGTAAGGAACAAGGTAATGAAAAGG
CCCATGGGGCCTCTGATGTTGTTCTCTACAAAATTGACGTCCCTGCCAATAGATATGACCTGCTGTGTCTGGAAGGATTG
GTTCGAGGACTTCAAGTCTTCAAAGAAAGGATAAAGACTCCGATGTATAAACGGGTAATGCCTAAAGGAGAAATCCAGAA
GTTGATCATCACAGAAGAGACAGCTAAAATACGCCCGTACACTGTTGCAGCGGTTCTCCGAAACATAAAGTTTACAAAAG
ATAGATATGACAGCTTCATTGAACTTCAGGAGAAATTACATCAGAACATTTGCAGGAAAAGAGCCTTGGTTGCTATTGGT
ACCCATGATTTGGACACTTTGTCAGGTCCATTTACTTACACTGCAAAGAAACCTTCTGATATCAAATTCAAGCCTCTAAA
TAAGAGTAAAGAGTATACAGCCTGTGAACTGATGAACATATACAAGACTGACAACCAGCTTAAACATTATTTACATATAA
TTGAAAATAAACCTCTGTACCCAGTTATCTATGATAGCAAAGGTGTCGTCCTTTCCATGCCTCCAATCATCAACGGAAAC
CATTCCAAAATAACAGTAAATACGAAAAATGTATTTATTGAGTGCACAGGAACTGACTTTACTAAGGCAAAAATAGTTCT
TGATGTCATTGTTACCACGTTCAGTGAATATTGTGAGAATCAGTTTACGGTTGAAGCAGCTGAGGTAGTTTTTCCTAATG
GAAAATTACATACCTTTCCAGAACTGGCTTATCGAAAGGAGATGGTGAGAGCTGACCTAATTAACAAAAAAGTTGGGATC
AGAGAAACTCCAGAAAATCTTGCCAAGCTTCTGACCAGGATGTGTTTAAAGTCAGAAGTCATAGGCGATGGGAATCAGAT
CGAGGTTGAAATCCCCCCGACCAGAGCTGACATTATCCACGCCTGTGATATCATAGAAGACGCAGCTATTGCTTACGGAT
ATAACAACATTCAGATGACTCTCCCGAAAACGTACACCATAGCTAATCAATTTCCCCTAAATAAACTCACAGAACTCCTG
AGACAGGACATGGCAGCTGCCGGATTCACCGAAGCACTTACCTTTGCTCTGTGCTCCCAAGAAGATATTGCTGACAAACT
GGGTATGGATATCTCTGCAACCAAGGCCGTCCACATAAGTAATCCTAAAACGGCTGAATTCCAGGTGGCACGCACTACCC
TTCTTCCTGGCCTCCTCAAGACCCTAGCTGCCAATCGGAAGACGCCACTTCCTCTGAAGCTGTTTGAAATTTCTGACATT
GTAATAAAAGATTCTAGCAGAGATGTGGGTGCAAGAAACTACAGGCATCTCTGTGCTGTTTATTACAACAAGAATCCTGG
GTTTGAGATAATCCATGGGCTTCTGGATAGAATCATGGAGCTGCTTGACGTGCCTCCTGGTGAAAAGAAGGGAGGATATG
CAATCAAAGCATCAGAAGGCCCTGTGTTCTTTCCTGGGCGATGTGCAGAGATCTTTGCCCGGGGCCAGAGCATCGGGAAG
CTGGGGGTCCTTCATCCCGACGTTATCACCAAGTTCGAGCTGACTATGCCCTGCTCCTGCGTGGAAATCAACATTGAGCC
ATTTTTG
ORF - retro_btau_1451 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.32 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPTVSVKRDLLFRALGRTYTDEEFDELCFEFGLELDEITSEKEIISKEQGNEKAHGASDVVLYKIDVPAN |
| MPTVSVK.DLLFRALGRTYTDEEFDELCFEFGLELDEITSEKEIISKEQGNEKAHGASDVVLYKIDVPAN | |
| Retrocopy | MPTVSVK*DLLFRALGRTYTDEEFDELCFEFGLELDEITSEKEIISKEQGNEKAHGASDVVLYKIDVPAN |
| Parental | RYDLLCLEGLVRGLQVFKERIKTPMYKRVMPKGEIQKLIITEETAKIRPYAVAAVLRNIKFTKDRYDSFI |
| RYDLLCLEGLVRGLQVFKERIKTPMYKRVMPKGEIQKLIITEETAKIRPY.VAAVLRNIKFTKDRYDSFI | |
| Retrocopy | RYDLLCLEGLVRGLQVFKERIKTPMYKRVMPKGEIQKLIITEETAKIRPYTVAAVLRNIKFTKDRYDSFI |
| Parental | ELQEKLHQNICRKRALVAIGTHDLDTLSGPFTYTAKKPSDIKFKPLNKSKEYTACELMNIYKTDNQLKHY |
| ELQEKLHQNICRKRALVAIGTHDLDTLSGPFTYTAKKPSDIKFKPLNKSKEYTACELMNIYKTDNQLKHY | |
| Retrocopy | ELQEKLHQNICRKRALVAIGTHDLDTLSGPFTYTAKKPSDIKFKPLNKSKEYTACELMNIYKTDNQLKHY |
| Parental | LHIIENKPLYPVIYDSKGVVLSMPPIINGNHSKITVNTKNVFIECTGTDFTKAKIVLDVIVTTFSEYCEN |
| LHIIENKPLYPVIYDSKGVVLSMPPIINGNHSKITVNTKNVFIECTGTDFTKAKIVLDVIVTTFSEYCEN | |
| Retrocopy | LHIIENKPLYPVIYDSKGVVLSMPPIINGNHSKITVNTKNVFIECTGTDFTKAKIVLDVIVTTFSEYCEN |
| Parental | QFTVEAAEVVFPNGKLHTFPELAYRKEMVRADLINKKVGIRETPENLAKLLTRMCLKSEVIGDGNQIEVE |
| QFTVEAAEVVFPNGKLHTFPELAYRKEMVRADLINKKVGIRETPENLAKLLTRMCLKSEVIGDGNQIEVE | |
| Retrocopy | QFTVEAAEVVFPNGKLHTFPELAYRKEMVRADLINKKVGIRETPENLAKLLTRMCLKSEVIGDGNQIEVE |
| Parental | IPPTRADIIHACDIIEDAAIAYGYNNIQMTLPKTYTIANQFPLNKLTELLRQDMAAAGFTEALTFALCSQ |
| IPPTRADIIHACDIIEDAAIAYGYNNIQMTLPKTYTIANQFPLNKLTELLRQDMAAAGFTEALTFALCSQ | |
| Retrocopy | IPPTRADIIHACDIIEDAAIAYGYNNIQMTLPKTYTIANQFPLNKLTELLRQDMAAAGFTEALTFALCSQ |
| Parental | EDIADKLGMDISATKAVHISNPKTAEFQVARTTLLPGLLKTLAANRKMPLPLKLFEISDIVIKDSSRDVG |
| EDIADKLGMDISATKAVHISNPKTAEFQVARTTLLPGLLKTLAANRK.PLPLKLFEISDIVIKDSSRDVG | |
| Retrocopy | EDIADKLGMDISATKAVHISNPKTAEFQVARTTLLPGLLKTLAANRKTPLPLKLFEISDIVIKDSSRDVG |
| Parental | ARNYRHLCAVYYNKNPGFEIIHGLLDRIMQLLDVPPGEKKGGYAIKASEGPVFFPGRCAEIFARGQSIGK |
| ARNYRHLCAVYYNKNPGFEIIHGLLDRIM.LLDVPPGEKKGGYAIKASEGPVFFPGRCAEIFARGQSIGK | |
| Retrocopy | ARNYRHLCAVYYNKNPGFEIIHGLLDRIMELLDVPPGEKKGGYAIKASEGPVFFPGRCAEIFARGQSIGK |
| Parental | LGVLHPDVITKFELTMPCSCVEINIEPFL |
| LGVLHPDVITKFELTMPCSCVEINIEPFL | |
| Retrocopy | LGVLHPDVITKFELTMPCSCVEINIEPFL |
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 |
|---|---|---|
| ERP005899_liver | 1 .23 RPM | 10 .24 RPM |
| ERP005899_muscle | 0 .32 RPM | 43 .81 RPM |
| SRP017611_brain | 1 .42 RPM | 19 .05 RPM |
| SRP017611_kidney | 0 .65 RPM | 23 .06 RPM |
| SRP017611_liver | 0 .76 RPM | 12 .76 RPM |
| SRP030211_testis | 0 .43 RPM | 31 .73 RPM |
Bos taurus was not studied using ChIP-Seq data.
13 EST(s) were mapped to retro_btau_1451 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| CB532909 | 35008720 | 35009110 | 97.7 | 381 | 9 | 372 |
| CK960751 | 35008997 | 35009693 | 100 | 696 | 0 | 696 |
| DY058326 | 35009393 | 35009664 | 100 | 271 | 0 | 271 |
| DY070806 | 35009374 | 35009597 | 100 | 223 | 0 | 223 |
| DY117886 | 35009312 | 35009663 | 100 | 351 | 0 | 351 |
| EE909578 | 35009105 | 35009629 | 100 | 524 | 0 | 524 |
| EE909826 | 35009105 | 35009712 | 100 | 607 | 0 | 607 |
| EE909830 | 35009105 | 35009564 | 100 | 459 | 0 | 459 |
| EE909852 | 35009105 | 35009684 | 100 | 578 | 0 | 578 |
| EW740015 | 35009050 | 35009230 | 98.4 | 177 | 3 | 174 |
| GO352920 | 35009050 | 35009228 | 99.5 | 177 | 1 | 176 |
| GO353727 | 35009050 | 35009228 | 99.5 | 177 | 1 | 176 |
| GO353770 | 35009228 | 35009723 | 99.8 | 494 | 1 | 493 |
Bos taurus was not studied using FANTOM5 data.
retro_btau_1451 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1451 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000011649 | 1 retrocopy |
retro_btau_1451 ,
|
| Felis catus | ENSFCAG00000026772 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000017051 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000006985 | 1 retrocopy |