RetrogeneDB ID: retro_sara_314

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_159565:4476..5082(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH13
• Ensembl ID: ENSSARG00000003600
• Aliases: None
• Description: retinol dehydrogenase 13 (all-trans/9-cis) [Source:HGNC Symbol;Acc:19978]

Sequence

>retro_sara_314
GAGCCTAGACTGGATGTCTTGATTAATAACGCAGGGGTCTTCCAGTGCCCTTATATGAAGACTGAAGATGGGTTTGAGAT
GCAGTTTGGAGTGAACCATCTCGGACACTTCCTGCTCACCAATCTACTCCTTGGGCTCCTGAAAAGTTCAGCTCCCAGCA
GGATTGTGGTCGTTTCTTCCAAGCTTTACAAATACGGAGACATCAACTTTGAAGACTTGAACAGTGAGCAAAGTTACAAT
AAAAGCTTTTGTTACAGCCGGAGCAAACTGGCTAATATTCTCTTTACTAGAGAACTCGCCCGCCGCCTAGAAGGCACCAA
TGTCACTGTCAATGTATTACACCCCGGGATTGTAAGGACTAACCTTGGGAGGCATATCCACATTCCCCTGTTGGCCAGGC
CACTTTTCAGTTTAGTGTCATGGGCGTTTTTCAAATCTCCTGCTGAAGGTGCCCAGACTTCAGTTTATTTGGCCTCTTCC
CCTGAGGTAGAAGGTGTTTCAGGGAAGTACTTTGGGGACTGTAAAGAAGAAGAACTATTGCCCAAAGCTATGGACGATTT
AGTTGCTAGAAAACTCTGGGATATCAGTGAAGTAATGGTCGGCTTA

Alignment

ORF - retro_sara_314 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.63 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEHVHVLINNAAVMCCPHWSTEDGFEMQFGVNHLGPFLLTNLLLDKLKASAPSRIINLSSLAHIAGHIDF
          E....VLINNA.V..CP...TEDGFEMQFGVNHLG.FLLTNLLL..LK.SAPSRI...SS.....G.I.F
Retrocopy EPRLDVLINNAGVFQCPYMKTEDGFEMQFGVNHLGHFLLTNLLLGLLKSSAPSRIVVVSSKLYKYGDINF

Parental  EDLNWQQRKFDTKAAYCQSKLAVVLFTKELSRRLQGTGVTVNALHPGVARTELGRHTGLHTSTFSSLTLG
          EDLN..Q........Y..SKLA..LFT.EL.RRL.GT.VTVN.LHPG..RT.LGRH...H..........
Retrocopy EDLNSEQ-SYNKSFCYSRSKLANILFTRELARRLEGTNVTVNVLHPGIVRTNLGRH--IHIPLLARPLFS

Parental  PIFWLLVKSPQLAAQPSTYLAVAEELEGVSGKYFDGFREKSPAAKAEDEEVAQRLWAESARLVGL
          ...W...KSP...AQ.S.YLA...E.EGVSGKYF....E.....KA.D..VA..LW..S...VGL
Retrocopy LVSWAFFKSPAEGAQTSVYLASSPEVEGVSGKYFGDCKEEELLPKAMDDLVARKLWDISEVMVGL

Legend:

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

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_314 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003306	1 retrocopy	retro_amel_114,
Equus caballus	ENSECAG00000023146	1 retrocopy	retro_ecab_338,
Ochotona princeps	ENSOPRG00000015998	2 retrocopies	retro_opri_286, retro_opri_524,
Petromyzon marinus	ENSPMAG00000009095	1 retrocopy	retro_pmar_3,
Pongo abelii	ENSPPYG00000010398	1 retrocopy	retro_pabe_1972,
Pan troglodytes	ENSPTRG00000011484	1 retrocopy	retro_ptro_1576,
Sorex araneus	ENSSARG00000003600	1 retrocopy	retro_sara_314 ,
Tupaia belangeri	ENSTBEG00000016531	1 retrocopy	retro_tbel_1570,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,