RetrogeneDB ID: retro_chof_561

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_121822:2769..3642(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000110
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000004899
• Aliases: None
• Description: None

Sequence

>retro_chof_561
ATGAAGTCCAGTCCTGCTATCCAAGCTGCCATTGACTTCACAGTGGGGGCTGCAGGGGGCACAGTGTGCGTGCTGACCAG
ACCCTTTGACAAGATGAAAGTGGAGATACAGATGTTTCCTGACCTGTACAGGGGGCTCACCAACTGCTGCCTCAAGACCT
ACTCTCAGGTGGGCTTCTGGGGCTTCTACAAGGGGACAAGCCCCGCACTAATCGCCAGCGTTGCCGGGAACTCTGTCCTT
TTCATGTGCTACATCATCTTCTAGCGGGTCTTAAGGAAGGTGGTTGGATTGGACAAGCAGGCAAAGCTGAGTGACCTGCA
GAATGCCACCGCCAGCTCCTTTGCTGTGCTGTCACTCTGCCCCACTGAGCTCGTGAAGTGCTGCCTGCAGACCCTGTACA
AGATGGAGATGTTGGGGAAGATCATCAAAAACCAAATGCAGTTGGGTCTTTTGTGAAGATCATCCTCTCAAAGGATGACC
CTGTGGGCTTCTACCAGGGTCTCTCTGGCACTTTACTTCGGGAAGTACCAAGCTATTTCTGTTTCTTCAGTGGCTATGAA
TTGAGCTGGACAGTTGTTGCATCAGGGAGATGAGATGAACTAGGCACTGCCCTCTGATGTTTGAGTTGGTGGAATTTGCT
TCTGGCTGACTATATACCCAGTGGATTGTATCAAATCCAGACTTCAGGTTCTTTCCATGGCTGGAAAACGGGTGGGGTTT
CTTAGAACCTTTGTGAGTGTCATGAAAAATGAAGGAATAACAGTCCTGTATTCTAGACTGAAGCCTACTATGATTCCCAC
ATTTCCTGCCAATGGAGCTCTGTTTTGGGCCTGTGAATACAGGAAGTTGATGATGAGCGAGTTCAAAGCATGC

Alignment

ORF - retro_chof_561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKSNPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFWGFYKGTSPA
          MKS.PAIQAAID.T.GAAGGT.CVLT..PFD.MKV..Q.FPDLYRGLT.CCLKTYSQVGFWGFYKGTSPA
Retrocopy MKSSPAIQAAIDFTVGAAGGTVCVLT-RPFDKMKVEIQMFPDLYRGLTNCCLKTYSQVGFWGFYKGTSPA

Parental  LIANIAENSVLFMCYGFCQQVVRKAAGLDRQAKLSDLQNATAGSFASAFAALVLCPTELVKCRLQAMYEM
          LIA..A.NSVLFMCY.....V.RK..GLD.QAKLSDLQNATA.SFA.....L.LCPTELVKC.LQ..Y.M
Retrocopy LIASVAGNSVLFMCYIIF*RVLRKVVGLDKQAKLSDLQNATASSFA----VLSLCPTELVKCCLQTLYKM

Parental  EMSGKIAKSH-NTVGSVVKSILTKDGPLGFYHGLSSTLLREVPGYFCFFGGYELSRSFFASGRSKDELGP
          EM.GKI.K...N.VGS.VK.IL.KD.P.GFY.GLS.TLLREVP.YFCFF.GYELS....ASGR..DELG.
Retrocopy EMLGKIIKNQ<NAVGSFVKIILSKDDPVGFYQGLSGTLLREVPSYFCFFSGYELSWTVVASGR-*DELGT

Parental  VPLMLS-GGVGGICLWLVVYPVDCIKSRIQVLSMAGKQAGFLGTFVSVVRNEGMKALYSGLKPTMIRAFP
          ....LS.GG....C.WL..YPVDCIKSR.QVLSMAGK..GFL.TFVSV..NEG...LYS.LKPTMI..FP
Retrocopy AL*CLS>GGI---CFWLTIYPVDCIKSRLQVLSMAGKRVGFLRTFVSVMKNEGITVLYSRLKPTMIPTFP

Parental  ANGALFLAYEYSRKLMMSQFEAC
          ANGALF.A.EY.RKLMMS.F.AC
Retrocopy ANGALFWACEY-RKLMMSEFKAC

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_561 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011723	1 retrocopy	retro_amel_5,
Bos taurus	ENSBTAG00000011647	1 retrocopy	retro_btau_1581,
Canis familiaris	ENSCAFG00000005955	1 retrocopy	retro_cfam_211,
Choloepus hoffmanni	ENSCHOG00000004899	3 retrocopies	retro_chof_1643, retro_chof_494, retro_chof_561 ,
Erinaceus europaeus	ENSEEUG00000014870	1 retrocopy	retro_eeur_329,
Mus musculus	ENSMUSG00000031482	1 retrocopy	retro_mmus_75,
Oryctolagus cuniculus	ENSOCUG00000016684	2 retrocopies	retro_ocun_192, retro_ocun_1927,
Ochotona princeps	ENSOPRG00000014616	1 retrocopy	retro_opri_7,
Rattus norvegicus	ENSRNOG00000011881	1 retrocopy	retro_rnor_130,
Sorex araneus	ENSSARG00000002472	1 retrocopy	retro_sara_30,
Sus scrofa	ENSSSCG00000009373	1 retrocopy	retro_sscr_688,