RetrogeneDB ID: | retro_btau_1713 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 9:88040353..88041486(-) | ||
| Located in intron of: | ENSBTAG00000015076 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.79166 | ||
| Ensembl ID: | ENSBTAG00000016174 | ||
| Aliases: | None | ||
| Description: | nucleolin [Source:RefSeq peptide;Acc:NP_001193589] |
Retrocopy-Parental alignment summary:
>retro_btau_1713
CCTGTCAAAGAAGCACCTGGAAAACAAAAGAAGGAAATGGCCAAACAAAAAGCAGCTCCTGAAGCCAAGAAACAAAAAGT
GGAAGGCACAGAACCAACTACGTCTTTCAATCTCTTTGTTGGAAACCTGAACTTCAATAAATCTGCTCCTGAATTGAAAA
CGGGTATCAGTGATCTTTTTGCTAAAAATGATTTTGCTGTTGTTGATGTCAGAATTGGTGTGTCTAGGAAGTTTGGCTAT
GTGGATTTTGAATCTGCCGAAGACCTGGAAAAAGCCTTGGAACTCACTGATTTAAAAGTCTTTGGCAATGAAATTAAACT
AGAAAAACCAGAGGGAAAAGACAGTAAGAAAGATTGAGATGCAAGAACACTTTTGGCTAAAAATCTGCCTTACAAAGTTA
CTCAGGATGAATTAAAAGAAGTGTTTGAAGATGCTGTGGAAATCAGATTAGTCAGCAAGGATGGAAAAAGTAAAGGGATT
GCTTATATTGAATTTAAGACAGAAGCTGATGCAGAAGAAACCTTGGAAGAAAAGCAGGGAACAGAGATAGATGGGCGATC
CATTTCTCTGTACTACACCGGAGAGAAAGGTCAAAGTCAAGACCATAGAGGTGGAAAGAATAGCACTTGGAGTGGTGAAT
GAAAAACCCTGGTTTTAAGCAACCTCTCCTATAGTGCAACCGAAGAAACTCTTAAGCAAGTATTTGAGAAGGCAACTCAT
ATCAAGGTGCCCCAGAACCAAAATGGCAAATCTAAAGGGTATGCATTTATAGAATTTGCTTCATTTGAAGATGCTAAAGA
AGCTTTAAATTCATGTAATAAAAGGGAAATTGAGGGCAGAGCCATCAGACTGGAGTTGCAAGGACCCAGGGGATCACCTA
ATGCAAGAAGCCAGCCATCCAAAACTCTCTTTGTCAAAGGTCTCTCTGAGGATACCACAGAAGAGACGTTAAAAGAGTCG
TTTGATGGCTGTATTCGAGCAAGGATAGTCACTGACCGGGAGACTGGATCCTCCGAAGGGTTTGGTTTTGTAGACTTCAA
CAGCGAGGAAGATGCCAAAGCTGCCAAGGAGGCCATGGAAGATGGTGAAACTGATGGAAACAAAGTCACTTTGGACTGGC
CAAACCTAAGGGT
ORF - retro_btau_1713 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.57 % |
| Parental protein coverage: | 52.5 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PVKEAPGKRKKEMAKQKAAPEAKKQKVEGTEPTTSFNLFVGNLNFNKSAPELKTGISDLFAKNDLAVVDV |
| PVKEAPGK.KKEMAKQKAAPEAKKQKVEGTEPTTSFNLFVGNLNFNKSAPELKTGISDLFAKND.AVVDV | |
| Retrocopy | PVKEAPGKQKKEMAKQKAAPEAKKQKVEGTEPTTSFNLFVGNLNFNKSAPELKTGISDLFAKNDFAVVDV |
| Parental | RIGVSRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKDRDARTLLAKNLPYKVTQDELKE |
| RIGVSRKFGYVDFESAEDLEKALELT.LKVFGNEIKLEKP.GKDSKKD.DARTLLAKNLPYKVTQDELKE | |
| Retrocopy | RIGVSRKFGYVDFESAEDLEKALELTDLKVFGNEIKLEKPEGKDSKKD*DARTLLAKNLPYKVTQDELKE |
| Parental | VFEDAVEIRLVSKDGKSKGIAYIEFKTEADAEKTLEEKQGTEIDGRSISLYYTGEKGQSQDHRGGKNSTW |
| VFEDAVEIRLVSKDGKSKGIAYIEFKTEADAE.TLEEKQGTEIDGRSISLYYTGEKGQSQDHRGGKNSTW | |
| Retrocopy | VFEDAVEIRLVSKDGKSKGIAYIEFKTEADAEETLEEKQGTEIDGRSISLYYTGEKGQSQDHRGGKNSTW |
| Parental | SGESKTLVLSNLSYSATEETLQEVFEKATHIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR |
| SGE.KTLVLSNLSYSATEETL..VFEKATHIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR | |
| Retrocopy | SGE*KTLVLSNLSYSATEETLKQVFEKATHIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR |
| Parental | AIRLELQGPRGSPNARSQPSKTLFVKGLSEDTTEETLKESFDGSIRARIVTDRETGSSKGFGFVDFNSEE |
| AIRLELQGPRGSPNARSQPSKTLFVKGLSEDTTEETLKESFDG.IRARIVTDRETGSS.GFGFVDFNSEE | |
| Retrocopy | AIRLELQGPRGSPNARSQPSKTLFVKGLSEDTTEETLKESFDGCIRARIVTDRETGSSEGFGFVDFNSEE |
| Parental | DAKAAKEAMEDGEIDGNKVTLDW-AKPKG |
| DAKAAKEAMEDGE.DGNKVTLDW.AKPKG | |
| Retrocopy | DAKAAKEAMEDGETDGNKVTLDW<AKPKG |
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 .00 RPM | 60 .13 RPM |
| ERP005899_muscle | 0 .26 RPM | 254 .65 RPM |
| SRP017611_brain | 0 .23 RPM | 165 .27 RPM |
| SRP017611_kidney | 0 .30 RPM | 188 .54 RPM |
| SRP017611_liver | 0 .00 RPM | 151 .17 RPM |
| SRP030211_testis | 0 .27 RPM | 292 .84 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1713 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1713 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1713 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000016174 | 1 retrocopy |
retro_btau_1713 ,
|
| Myotis lucifugus | ENSMLUG00000014547 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000027852 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000009094 | 2 retrocopies |