RetrogeneDB ID: | retro_btau_1105 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 26:37282718..37285097(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000039671 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.88705 | ||
| Ensembl ID: | ENSBTAG00000008390 | ||
| Aliases: | None | ||
| Description: | dnaJ homolog subfamily C member 10 [Source:RefSeq peptide;Acc:NP_001092591] |
Retrocopy-Parental alignment summary:
>retro_btau_1105
ATGGGAGTCTGGTTAAATAAAGATGACTATGTCAGAGACTTGAAAAGGGTCATGCTCTTTTTTCTAGTAATGTATATGGC
CATTTTAGTGGGTACAGATCAGGATTTTTACAGTTTACTTGGAGTATCCAAAACTGCAAGCAGTAGAGAAATAAGACAAG
CTTTCAAGAAATTGGCATTGAAGCTACATCCTGATAAAAACCCGAATAACCCAAATGCACATAGTGATTTTTTGAAAGTA
AATAGAGCATATGAAGTACTCAAAGATGAAGATCTGCGGAAAAAATACGACAAATATGGAGAAAAGGGACTTGCAGATAA
TCAAGGAGGCCAGTATGAAAGCTGGAATTACTACCGTTATGATTTTGGTATTTATGATGATGATCCTGAAATCATAACAT
TGGATAGAAGAGAATTTGATGCTGCTGTTAATTCTGGAGAACTGTGGTTTGTGAACTTTTACTCCCCAGGGTGTTCACAC
TGCCATGATTTAGCTCCCACATGGAGAGACTTTGCAAAAGTAGTAGATGGATTGCTTCGAATTGGAGCAGTTAACTGTGG
CGATGATAGAATGCTTTGCCGAATGAAAGGAGTCAACAGTTATCCCAGCCTTTTCATTTTTAGGTCTGGAATGGCTGCAG
TGAAATACCATGGTGACAGATCAAAGGAAAGTTTAATGAATTTCGCCATGCAGCATGTTAGAAGCACAGTGACAGAATTA
TGGACAGGAAATTTTGTTAACTCCATACAAACTGCATTTGCTGCTGGTATTGGCTGGCTGATCACTTTTTGTTCCGAAGG
AAGCGATTGTTTGACCTCACAGACACGTCTCAGGTTAAGTGGTATGTTGGATGGTCTTGTTAATGTGGGATGGGTGGACT
GTGCCACCCAGGACAACCTTTGTAAAAGTTTGGATATTACAACAAGTACGACTGCCTATTTTCCTCCTGGAGCCACTTTA
AATAACAAAGAGAAAAGCGGTATTTTGTTTCTTAATTCATTGGATGCTAAAGAAATTTATTTGGAAATAATGCATAATCT
TCCAGATTTTGAACTCCTTTCAGCAAATTCACTACAGGATCGTTTAGCTCATCATCGGTGGCTCTTATTTTTTCAATTTG
GACAAAATGAAAATTCAAATGATCCTGAGTTGAAGAAACTAAAAACTCTACTTAAAAATGAACATATTCAAATTGGCAAG
TTTGACTGTTCCTCTGCACCAGACGTCTGTAGTAACTTCTATGTTTTTCAGCCATGTCTAGCAGTATTTAAAGGACAGGG
AACCAAAGAATTTGAAATTCATCATGGAAAGAAGATTCTATATGACATACTTGCCCTTGCCAAGGAAAGTGTCAATTCTC
ATGTTACCACACTTGGACCTCAAAATTTTCCTGCCAATGAAAAAGAACCATGGCTAGTTGATTTTTTTGCCCCTTGGTGT
CCACCATGTCGAGCTTTATTGCCAGAGCTGCGAAAAGCATCAAAGCATCTTTATGGTCAGCTTAAGTTTGGTACATTAGA
CTGTACAATTCATGAAGGACTCTGTAACATGTATAACATTCAGGCTTATCCAACAACAGTGGTATTCAACCAGTCCAACA
TTCATGAATATGAAGGACATCACTCTGCTGAACAGATCTTGGAGTTCGTAGAGGATCTTATGAATCCTTCAGTGATCTCT
TTGACACCTACCACTTTCAACGAACTGGTTAAACAAAGAAAGCATGATGAAGTCTGGATGGTTGATTTCTATTCTCCATG
GTGTCATCCATGTCAAATCTTAATGCCAGAATGGAAAAGAATGGCCCGGACATTAATTGGACTGATCAATGTGGGCAGTA
TAGACTGCCAACAGTATCATTCTTTTTGTGCCCAAGAAAATGTTCGGAGATACCCTGAGATAAGATTTTTTCCCCAAAAA
TCAAATAAAGCTTATGAATATCATAGTTACAATGGTTGGAATAGAGATGCTTATTCCCTAAGAATCTGGGGTCTAGGATT
TTTACCTCAAGCATCTATAGATCTAACACCTCAGACTTTCAATGAAAAGGTTTTACAAGGGAAAAACCATTGGGTGGTTG
ATTTCTATGCTCCTTGGTGTGGACCTTGCCAGAACTTTGCTCCAGAGTTTGAGCTCTTGGCTAGGACACTTAAAGGAAAA
GTAAAAGCTGGAAAAGTAGACTGTCAGGCTTATGCTCAAACTTGCCAGAAAGCTGGTATCAGAGCCTATCCGACTGTGAG
ATTGTATCCTTATGAAAGGGCAAAGAGAAATACTTGGGGAGAGCAAATAGACTCTAGAGATGCAAAAGAGATTGCTACCT
TAATATATGAAAAATTGGAAAAGCTCCAAAATCATGAGAAAAGAGATAAGGACGAACTT
ORF - retro_btau_1105 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.24 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MGVWLNKDDYVRDLKRVMLFFLVMYMAILVGTDQDFYSLLGVSKTASSREIRQAFKKLALKLHPDKNPNN |
| MGVWLNKDDYVRDLKRVMLFFLVMYMAILVGTDQDFYSLLGVSKTASSREIRQAFKKLALKLHPDKNPNN | |
| Retrocopy | MGVWLNKDDYVRDLKRVMLFFLVMYMAILVGTDQDFYSLLGVSKTASSREIRQAFKKLALKLHPDKNPNN |
| Parental | PNAHSDFLKVNRAYEVLKDEDLRKKYDKYGEKGLADNQGGQYESWNYYRYDFGIYDDDPEIITLDRREFD |
| PNAHSDFLKVNRAYEVLKDEDLRKKYDKYGEKGLADNQGGQYESWNYYRYDFGIYDDDPEIITLDRREFD | |
| Retrocopy | PNAHSDFLKVNRAYEVLKDEDLRKKYDKYGEKGLADNQGGQYESWNYYRYDFGIYDDDPEIITLDRREFD |
| Parental | AAVNSGELWFVNFYSPGCSHCHDLAPTWRDFAKEVDGLLRIGAVNCGDDRMLCRMKGVNSYPSLFIFRSG |
| AAVNSGELWFVNFYSPGCSHCHDLAPTWRDFAK.VDGLLRIGAVNCGDDRMLCRMKGVNSYPSLFIFRSG | |
| Retrocopy | AAVNSGELWFVNFYSPGCSHCHDLAPTWRDFAKVVDGLLRIGAVNCGDDRMLCRMKGVNSYPSLFIFRSG |
| Parental | MAAVKYHGDRSKESLMNFAMQHVRSTVTELWTGNFVNSIQTAFAAGIGWLITFCSEGSDCLTSQTRLRLS |
| MAAVKYHGDRSKESLMNFAMQHVRSTVTELWTGNFVNSIQTAFAAGIGWLITFCSEGSDCLTSQTRLRLS | |
| Retrocopy | MAAVKYHGDRSKESLMNFAMQHVRSTVTELWTGNFVNSIQTAFAAGIGWLITFCSEGSDCLTSQTRLRLS |
| Parental | GMLDGLVNVGWVDCATQDNLCKSLDITTSTTAYFPPGATLNNKEKSGILFLSSLDAKEIYLEIMHNLPDF |
| GMLDGLVNVGWVDCATQDNLCKSLDITTSTTAYFPPGATLNNKEKSGILFL.SLDAKEIYLEIMHNLPDF | |
| Retrocopy | GMLDGLVNVGWVDCATQDNLCKSLDITTSTTAYFPPGATLNNKEKSGILFLNSLDAKEIYLEIMHNLPDF |
| Parental | ELLSANSLQDRLAHHRWLLFFQFGQNENSNDPELKKLKTLLKNEHIQIGKFDCSSAPDVCSNFYVFQPCL |
| ELLSANSLQDRLAHHRWLLFFQFGQNENSNDPELKKLKTLLKNEHIQIGKFDCSSAPDVCSNFYVFQPCL | |
| Retrocopy | ELLSANSLQDRLAHHRWLLFFQFGQNENSNDPELKKLKTLLKNEHIQIGKFDCSSAPDVCSNFYVFQPCL |
| Parental | AVFKGQGTKEFEIHHGKKILYDILAFAKESVNSHVTTLGPQNFPANEKEPWLVDFFAPWCPPCQALLPEL |
| AVFKGQGTKEFEIHHGKKILYDILA.AKESVNSHVTTLGPQNFPANEKEPWLVDFFAPWCPPC.ALLPEL | |
| Retrocopy | AVFKGQGTKEFEIHHGKKILYDILALAKESVNSHVTTLGPQNFPANEKEPWLVDFFAPWCPPCRALLPEL |
| Parental | RKASKHLYGQLKFGTLDCTVHEGLCNMYNIQAYPTTVVFNQSNIHEYEGHHSAEQILEFVEDLMNPSVIS |
| RKASKHLYGQLKFGTLDCT.HEGLCNMYNIQAYPTTVVFNQSNIHEYEGHHSAEQILEFVEDLMNPSVIS | |
| Retrocopy | RKASKHLYGQLKFGTLDCTIHEGLCNMYNIQAYPTTVVFNQSNIHEYEGHHSAEQILEFVEDLMNPSVIS |
| Parental | LTPTTFNELVKQRKHDEVWMVDFYSPWCHPCQVLMPEWKRMARTLIGLINVGSIDCQQYHSFCAQENVRR |
| LTPTTFNELVKQRKHDEVWMVDFYSPWCHPCQ.LMPEWKRMARTLIGLINVGSIDCQQYHSFCAQENVRR | |
| Retrocopy | LTPTTFNELVKQRKHDEVWMVDFYSPWCHPCQILMPEWKRMARTLIGLINVGSIDCQQYHSFCAQENVRR |
| Parental | YPEIRFFPQKSNKAYEYHSYNGWNRDAYSLRIWGLGFLPQASIDLTPQTFNEKVLQGKNHWVVDFYAPWC |
| YPEIRFFPQKSNKAYEYHSYNGWNRDAYSLRIWGLGFLPQASIDLTPQTFNEKVLQGKNHWVVDFYAPWC | |
| Retrocopy | YPEIRFFPQKSNKAYEYHSYNGWNRDAYSLRIWGLGFLPQASIDLTPQTFNEKVLQGKNHWVVDFYAPWC |
| Parental | GPCQNFAPEFELLARTLKGKVKAGKVDCQAYAQTCQKAGIRAYPTVRLYPYERAKRNTWGEQIDSRDAKE |
| GPCQNFAPEFELLARTLKGKVKAGKVDCQAYAQTCQKAGIRAYPTVRLYPYERAKRNTWGEQIDSRDAKE | |
| Retrocopy | GPCQNFAPEFELLARTLKGKVKAGKVDCQAYAQTCQKAGIRAYPTVRLYPYERAKRNTWGEQIDSRDAKE |
| Parental | IATLIYEKLEKLQNHEKRDKDEL |
| IATLIYEKLEKLQNHEKRDKDEL | |
| Retrocopy | IATLIYEKLEKLQNHEKRDKDEL |
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 | 0 .43 RPM | 13 .19 RPM |
| ERP005899_muscle | 0 .95 RPM | 80 .98 RPM |
| SRP017611_brain | 2 .28 RPM | 44 .86 RPM |
| SRP017611_kidney | 1 .96 RPM | 56 .19 RPM |
| SRP017611_liver | 0 .83 RPM | 13 .52 RPM |
| SRP030211_testis | 3 .55 RPM | 161 .90 RPM |
Bos taurus was not studied using ChIP-Seq data.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1105 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1105 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000001928 | 1 retrocopy | |
| Bos taurus | ENSBTAG00000008390 | 1 retrocopy |
retro_btau_1105 ,
|
| Felis catus | ENSFCAG00000026076 | 1 retrocopy |