RetrogeneDB ID: retro_tgut_23

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: 3:97276987..97278144(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SHCBP1
• Ensembl ID: ENSTGUG00000008933
• Aliases: None
• Description: SHC SH2-domain binding protein 1 [Source:HGNC Symbol;Acc:29547]

Sequence

>retro_tgut_23
GACTCTTGGAGTGACTATGGCAGTTGTGACGAACCACGGGCTGCTTTGGGAGGGACTGTATCAGACGGGATCATGCTTTT
CCCAGATATTTTTCACACCAGTCATCTTTTGTTTTACGACTGATTTAGTGCTTACCAGGATTATATCTTGGCTGACTGCA
AAACTTCTGAGGTGAAGTAGTTCATAGCTGGGTACCTGGAAAAGGTCCTTGAGCCCTCTGGCTGGCAGGCGATCTGGCGC
ACTAATGTGTTTGAGGTCCTCGTTGGGGTGGCTGATGTGAATTTCCTGGCCCTGAAGGCAGTTGTGCAGCTCAGTGAGCC
ATTCCTGTGTGAGTCCCAGGACAGCAGCTTTACCGTGGAGTGCATGAAGGAGCTTCTGGAGCTGAAGGAACATCAGATCC
TGCTGCAGGAGCTGTGGTTATATATTATGAGTCAGGAGAGTTTGACTAGACAGCACTAGCCATAGAGCATGTCAGGTTTT
TCTACCAGTACATCTGGAGGACCTGGGGCGAGGAGGAGGATGAGTTTGATTATTTTGCGCGATGTGTTGAGCCCTGACTG
AGACTGCACTATGACATCCTGGAACAGCGGGTGCCTTCTGGGCTGGTAGTTGATTACCAGAACTTATTATTTCAATGTGA
AGAGCTTTATGAGAAGTTTTTAAATGTGAGGAACAGCATCTCAAGCAATGATTCAGACTCAGAAGCAGAAAATGTTTCCA
TGGTGGAAGGACTAGAATTGTATGACAAAGTAGAGCACATAAAACAAAGGCTAAAACTAATTGAGACTCCTCTGCTGAGA
TATGTGTTTGGTTACCAAAAATATGGTAGCCTCCAGGCTACAGGACCGAGATCAACAGGTGCCAAGGTCATTCATGTTGT
GCCCTGGATCATGACAGCAAATCTGCTCCAGCTGTTGACAAGAGACAAACTTTGCCCAGAATCTTGTGATGCCTTAAAAG
TACAGTTTCACCGTGATCCACTAGCAGCTGTAAATGCCTGTTATGAAGGAGAGAGAGTCATCATCTATCCTGGCCATTAT
TTTGTTGATGGCATGTTCTCCATTGCTGATTCAGTAGAGCTAGAAGGCTATGGCCTGCCAGATGACGTTGTGATAGAAAA
ATAAGGGAGAGGAGATGACTTCTTTGACTGTACAGGT

Alignment

ORF - retro_tgut_23 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.57 %
• Parental protein coverage: 61.53 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSWSDYDCRDKPGTALERTVPDGNVRLPDIFHTNHLLFYDRFSAYQDYILSDCKASEVKQFIAEYLEKVL
          DSWSDY...D.P..AL..TV.DG....PDIFHT.HLLFYD.FSAYQDYIL.DCK.SEVK.FIA.YLEKVL
Retrocopy DSWSDYGSCDEPRAALGGTVSDGIMLFPDIFHTSHLLFYD*FSAYQDYILADCKTSEVK*FIAGYLEKVL

Parental  EPSGWQAIWRTNVFEVVVRVVDVNFPALKAVVQLSEPFLCESQDSSFTLECMQELLELKEHQILLQELW-
          EPSGWQAIWRTNVFEV.V.V.DVNF.ALKAVVQLSEPFLCESQDSSFT.ECM.ELLELKEHQILLQELW.
Retrocopy EPSGWQAIWRTNVFEVLVGVADVNFLALKAVVQLSEPFLCESQDSSFTVECMKELLELKEHQILLQELW<

Parental  VVYDESEKFDQTALAIEHVRFFYQYIWRTWDEEEEDEFDYFVRCVEPRLRLHYDILEQRVPSGLVVDYQN
          V.Y.ES..FD.TALAIEHVRFFYQYIWRTW.EEE.DEFDYF.RCVEP.LRLHYDILEQRVPSGLVVDYQN
Retrocopy VIYYESGEFD*TALAIEHVRFFYQYIWRTWGEEE-DEFDYFARCVEP*LRLHYDILEQRVPSGLVVDYQN

Parental  LLSQCEELYDKFLNVRNSISGNDSDSEAGNVSMVEGLKLYDQVEHIKQRLKLIETPLLRYVFGYQKYGSL
          LL.QCEELY.KFLNVRNSIS.NDSDSEA.NVSMVEGL.LYD.VEHIKQRLKLIETPLLRYVFGYQKYGSL
Retrocopy LLFQCEELYEKFLNVRNSISSNDSDSEAENVSMVEGLELYDKVEHIKQRLKLIETPLLRYVFGYQKYGSL

Parental  QSKGPRSAGAKVIHVVPLTITANLLQLLTRDKLCPESSEALEVQFYSDPLAAVNACYEGERVIICPGHYF
          Q..GPRS.GAKVIHVVP...TANLLQLLTRDKLCPES..AL.VQF..DPLAAVNACYEGERVII.PGHYF
Retrocopy QATGPRSTGAKVIHVVPWIMTANLLQLLTRDKLCPESCDALKVQFHRDPLAAVNACYEGERVIIYPGHYF

Parental  VDGMFSIADSVELEGYGLPDDVVIEKQGKGDNFFDCTG
          VDGMFSIADSVELEGYGLPDDVVIEK.G.GD.FFDCTG
Retrocopy VDGMFSIADSVELEGYGLPDDVVIEK*GRGDDFFDCTG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Taeniopygia guttata was not studied using RNA-Seq expression data.

ChIP-Seq

Taeniopygia guttata was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tgut_23 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_23 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_23 has 0 orthologous retrocopies within neognath group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Taeniopygia guttata	ENSTGUG00000008933	1 retrocopy	retro_tgut_23 ,