RetrogeneDB ID: retro_etel_872

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_178274:1314..2013(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000013742
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TSPAN3
• Ensembl ID: ENSETEG00000010916
• Aliases: None
• Description: tetraspanin 3 [Source:HGNC Symbol;Acc:17752]

Sequence

>retro_etel_872
CAGTGTGTTGTCACCTCCTTCAAAACTGTGCTGGTCTTTCTCAACCTCATCTTTTAGTGCAGAGGGCATTCTGTACTATG
TGGGGCCCTGTCTTTATCACTTATGAAGATTATGACCACAACTTTGGAAACATGCACATTCTCATTCCTGCTGTGGCAAT
CACCACTGTGGGAGCCCTGCTTTCCATCATTGGGTTAAATGGCTACTGCACCATGATCCCTGAAAGCCACTGTGGACTTG
CCACATTTTTCATCATCCTACTCTTGGATTTTGTCACAGAAGTCGGCATAGTGGTGCTGGGATATCTTTATAGAGCAAAG
GTGGAGAATGAAGTCAACCATGGTATTCAGAAATTCTATAAGGCCTACAAGGAAATCAATCCTGACACTTCTAGCCAGGC
TATTGATTATGAACAGAGACATCTTCACTGTTGTGGAATTCACAACTACTCAAACTGGGAAAACACAGACTGGTTCAAAG
AAACCAAAAACCAGAACATTCCTCTCAGTTGCTATAGGGAGCAGGCTCCCAGTTGTAACAGCAGTCTGGACCACCCCTCT
GACCGCTATGCCTAGGAGTGTGAGGCTATAGTTGTGAAGAAATTATAAGGAAATCATGATGAATGTGATCTGGGTCATGC
TGTCCTTTGAAACTCTTCAGCAGCTGGACATGCTGTGTACCTGCATCGTGCCGTGCAGA

Alignment

ORF - retro_etel_872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.81 %
• Parental protein coverage: 92.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QCGITS-STVLAFLILIWGAAG-ILCYVGAYVFITYDDYDHFFEDVYTLIPAVVIIAVGALLFIIGLIGC
          QC..TS..TVL.FL.LI....G...C.....VFITY.DYDH.F.....LIPAV.I..VGALL.IIGL.G.
Retrocopy QCVVTSFKTVLVFLNLIF*CRG<AFCTMWGPVFITYEDYDHNFGNMHILIPAVAITTVGALLSIIGLNGY

Parental  CATIRESHCGLATFVAILLLVFVTEVVVVVLGYVYRAKVENEVDRSIQKVYKTYNGTNPDAASRAIDYVQ
          C..I.ESHCGLATF..ILLL.FVTEV..VVLGY.YRAKVENEV...IQK.YK.Y...NPD..S.AIDY.Q
Retrocopy CTMIPESHCGLATFFIILLLDFVTEVGIVVLGYLYRAKVENEVNHGIQKFYKAYKEINPDTSSQAIDYEQ

Parental  RQLRCCGIHNYSDWENTDWFKETKNQSVPLSCCRETAPSCNGSLAHPSDLYAEGCEALVVKKL-QEIMMH
          R.L.CCGIHNYS.WENTDWFKETKNQ..PLSC.RE.APSCN.SL.HPSD.YA..CEA.VVKKL..EIMM.
Retrocopy RHLHCCGIHNYSNWENTDWFKETKNQNIPLSCYREQAPSCNSSLDHPSDRYA*ECEAIVVKKL>KEIMMN

Parental  VIWAALAFAAIQLLGMLCACIVLCR
          VIW..L.F...Q.L.MLC.CIV.CR
Retrocopy VIWVMLSFETLQQLDMLCTCIVPCR

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_872 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009727	1 retrocopy	retro_amel_1275,
Bos taurus	ENSBTAG00000002415	2 retrocopies	retro_btau_1089, retro_btau_1650,
Canis familiaris	ENSCAFG00000018068	2 retrocopies	retro_cfam_1391, retro_cfam_571,
Choloepus hoffmanni	ENSCHOG00000003785	2 retrocopies	retro_chof_162, retro_chof_1682,
Dasypus novemcinctus	ENSDNOG00000005619	3 retrocopies	retro_dnov_1371, retro_dnov_1520, retro_dnov_1616,
Echinops telfairi	ENSETEG00000010916	1 retrocopy	retro_etel_872 ,
Echinops telfairi	ENSETEG00000012276	1 retrocopy	retro_etel_1987,
Felis catus	ENSFCAG00000025746	1 retrocopy	retro_fcat_1860,
Mustela putorius furo	ENSMPUG00000017332	2 retrocopies	retro_mputfur_1641, retro_mputfur_1651,
Pteropus vampyrus	ENSPVAG00000004662	1 retrocopy	retro_pvam_394,
Ictidomys tridecemlineatus	ENSSTOG00000005615	1 retrocopy	retro_itri_1268,