RetrogeneDB ID: | retro_btau_278 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 1:112709719..112710303(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TBCB | ||
| Ensembl ID: | ENSBTAG00000015004 | ||
| Aliases: | TBCB, CKAP1 | ||
| Description: | Tubulin-folding cofactor B [Source:UniProtKB/Swiss-Prot;Acc:Q5E951] |
Retrocopy-Parental alignment summary:
>retro_btau_278
AGCTGTATGGACCTGTTCTACTGCAAGTTCTACGACAAGTTCTGCTGCAAGCTGGATCAGGATGATGCGTTGCTGGGCTC
CTACCCCATAGACGACAGCTGTCGCATCCATGTCATTGACCACAGCGGTGCCTGCCTTGGGGAGTATGAGGACATATCCA
AGGTGGAGAAATACGAGATCTCACAAGAAGCCTATGAACAGAGGCAAGACGCAATCCGCTCCTTCCTGAAGTGCAACAAG
CTAGGTTGATTCAATGAAGAAGAGCGGGCCCAGCAAGAGGCCGAGAACTCCCAGCACCTTATTGAGGAGGCAGCCCAGGC
CAGCACCATCCCTGTGGGCAGCCACTGTGAGGTGCAGACACCTGGGCAGCCCCCTCGCAGGGGCACCGTCATGTATGTAG
GACTGACAGATTTCAAACCTGGCTACTGGATTGGTGTCCACTATGATGAACCACTAGGGAAAAACGATGGCAGCGTGAAT
AGAAAACACTACTTTGAATGCCAGGCCAAGTAGGCGCCTTCGTCAAGCCATCAGTCATGACATTGGGGGACTTCCCTGAA
GAGGACTACGGTTTGGATGAGATG
ORF - retro_btau_278 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.67 % |
| Parental protein coverage: | 79.92 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SCMELELYGPDDKFCCKLDQDDALLGSYPVDDGCRIHVIDHSGARLGEYEDISKVEKYEISQEAYEQRQD |
| SCM..............LDQDDALLGSYP.DD.CRIHVIDHSGA.LGEYEDISKVEKYEISQEAYEQRQD | |
| Retrocopy | SCMDXXXXXXXXXXXXXLDQDDALLGSYPIDDSCRIHVIDHSGACLGEYEDISKVEKYEISQEAYEQRQD |
| Parental | SIRSFLKRNKLGRFNEEERAQQEAENSQRLIEEEAQASTIPVGSRCEVRTPGQPPRRGTVMYVGLTDFKP |
| .IRSFLK.NKLG.FNEEERAQQEAENSQ.LIEE.AQASTIPVGS.CEV.TPGQPPRRGTVMYVGLTDFKP | |
| Retrocopy | AIRSFLKCNKLG*FNEEERAQQEAENSQHLIEEAAQASTIPVGSHCEVQTPGQPPRRGTVMYVGLTDFKP |
| Parental | GYWIGIRYDEPLGKNDGSVNGKRYFECQAK-YGAFVKPSVVTVGDFPEEDYGLDEM |
| GYWIG..YDEPLGKNDGSVN.K.YFECQAK..GAFVKPSV.T.GDFPEEDYGLDEM | |
| Retrocopy | GYWIGVHYDEPLGKNDGSVNRKHYFECQAK<VGAFVKPSVMTLGDFPEEDYGLDEM |
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 .14 RPM | 5 .98 RPM |
| ERP005899_muscle | 0 .05 RPM | 29 .35 RPM |
| SRP017611_brain | 0 .37 RPM | 32 .62 RPM |
| SRP017611_kidney | 0 .06 RPM | 28 .45 RPM |
| SRP017611_liver | 0 .08 RPM | 9 .06 RPM |
| SRP030211_testis | 0 .32 RPM | 59 .45 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_278 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_278 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_278 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000015004 | 1 retrocopy |
retro_btau_278 ,
|
| Macaca mulatta | ENSMMUG00000000523 | 1 retrocopy |