RetrogeneDB ID: retro_chof_1562

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_325794:233..1352(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMCL1
• Ensembl ID: ENSCHOG00000012306
• Aliases: None
• Description: germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]

Sequence

>retro_chof_1562
AGTGCTGTGCCACCACCGCGGGGGAGCCGAGCCCAGCAGGAGCCGGGTTCCGGGGCGGGGCTTGACCAGGAGGCCAGGGC
TGGCGGCGGCGCTGTGGGCCACGGTGTCTGTGACTGCCCGGGCAGCCGCAGGCGCAAGCGGAGCAGCGGGGCCTTCTGCT
ACTGCCACCCCGACTCCAAGTTGGACAAGGATGAAGAAGGGGACGAGCAGCAGCGGCTCCTCAACACCCCGTGAAGGAAA
AAATTAAAGTGTGCATCCAAATATGCTTATCAAACATTGTTTTAGAATGGTGAAAACAGTGACATTAAGATTTGTGCTCT
AGGAGAAGAGTGGAGCTTACACAAAATGTATTTATGTCAATCTGGCTACTTTTCTAGTATGTTCAGTGGTTCTTGGAAAG
AATCCAGCATGAATATTATTGAACTGGAGATTCCTGACGAGAATATTGATATAGAAGCATTGCAGGTTGCATTTGGTTCA
CTCCCTAGAGATGGCCTCATAATAAAGCCCAATCGTGTTATTGCCATTTTGGCAGCAGCTTGTGTGCTGCAGTCGGATGG
TTTAATACAGCAATGTGGAGAGACAATGAAGGAAACAATTAATGTGAAAACTGCATGTGGCTATTATTTATCAGCAGGGA
CCTATGGATTAGATTCTGTAAAGAAAAAGTGCCTTGAATGGCTTCTAAACAATTTAATGACTCACCAGAATATTGAACTT
TTTAAAGAATTCAGTGTAAGTGTCATGAAACAGCTCATCAGTTCATCTAACTTATTTGTAATGCAAGTGGGAATGGATGT
ATACACAGCTCTTAAAAGGTGGATGTTCCTTTAACTTGTGCCTTCTTAGAATGGATCTTTAAAACAGCTTTTGACTGAAA
CAGATGCGTGGTTTTCTAAGCAGAAAAAAGATTTTGAAGATATGACCTTCCTTGAAACTGAGCAAGGAAAACCAGTTGTG
TCAATATTCGGACATTTAAGGTTCCAGTATATTATCACTGACCTGGCTTTCGCAAGAATTATTGAACAAGATTCTCTAGT
ACCTTCAGAATGGCTATCTTCTGTATGTAAACAGCAGTGACTTGCTATGCTCCGGGCAGAACAAGACCGTGAGGTGGGG

Alignment

ORF - retro_chof_1562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.73 %
• Parental protein coverage: 73.1 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRVLRPGGARAQQEPGSGAGGSARRPGAGGDAAGHGFCYCPGSLKRKRSSGAFCYCHPDSETDEDEEEGD
          S.V..P.G.RAQQEPGSGAG.......AGG.A.GHG.C.CPGS..RKRSSGAFCYCHPDS..D.D.EEGD
Retrocopy SAVPPPRGSRAQQEPGSGAG-LDQEARAGGGAVGHGVCDCPGSRRRKRSSGAFCYCHPDSKLDKD-EEGD

Parental  EQQRLLNTPRRKKLKSTSKYIYQTLFLNGENSDIKICALGEEWSLHKIYLCQSGYFSSMFSGSWKESSMN
          EQQRLLNTP.RKKLK..SKY.YQTLF.NGENSDIKICALGEEWSLHK.YLCQSGYFSSMFSGSWKESSMN
Retrocopy EQQRLLNTP*RKKLKCASKYAYQTLF*NGENSDIKICALGEEWSLHKMYLCQSGYFSSMFSGSWKESSMN

Parental  IIELEIPDQNIDIEALQVAFGSLYRDDVLIKPSRVIAILAAACMLQLDGLIQQCGETMKETINVKTVCGY
          IIELEIPD.NIDIEALQVAFGSL.RD...IKP.RVIAILAAAC.LQ.DGLIQQCGETMKETINVKT.CGY
Retrocopy IIELEIPDENIDIEALQVAFGSLPRDGLIIKPNRVIAILAAACVLQSDGLIQQCGETMKETINVKTACGY

Parental  YTSAGTYGLDSVKKKCLEWLLNNLMTHQNVELFKELSISVMKQLINSSNLFVMQVEMDVYTALKKWMFLQ
          Y.SAGTYGLDSVKKKCLEWLLNNLMTHQN.ELFKE.S.SVMKQLI.SSNLFVMQV.MDVYTALK.WMFL.
Retrocopy YLSAGTYGLDSVKKKCLEWLLNNLMTHQNIELFKEFSVSVMKQLISSSNLFVMQVGMDVYTALKRWMFL*

Parental  LVPSWNGSLKQLLTETDVWFSKWKKDFEGTTFLETEQGKPFVPVFRHLRLQYIISDLASARIIEQDSLIP
          LVPS.NGSLKQLLTETD.WFSK.KKDFE..TFLETEQGKP.V..F.HLR.QYII.DLA.ARIIEQDSL.P
Retrocopy LVPS*NGSLKQLLTETDAWFSKQKKDFEDMTFLETEQGKPVVSIFGHLRFQYIITDLAFARIIEQDSLVP

Parental  SEWLSSVYKQQWLAMLRAEQDSEVG
          SEWLSSV.KQQ.LAMLRAEQD.EVG
Retrocopy SEWLSSVCKQQ*LAMLRAEQDREVG

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_1562 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 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016116	1 retrocopy	retro_amel_1915,
Choloepus hoffmanni	ENSCHOG00000012306	2 retrocopies	retro_chof_1562 , retro_chof_802,
Equus caballus	ENSECAG00000016813	2 retrocopies	retro_ecab_1109, retro_ecab_899,
Homo sapiens	ENSG00000087338	1 retrocopy	retro_hsap_3407,
Loxodonta africana	ENSLAFG00000002565	3 retrocopies	retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus	ENSMLUG00000009183	2 retrocopies	retro_mluc_1521, retro_mluc_31,
Macaca mulatta	ENSMMUG00000000858	1 retrocopy	retro_mmul_98,
Mus musculus	ENSMUSG00000001157	1 retrocopy	retro_mmus_3665,
Nomascus leucogenys	ENSNLEG00000010132	1 retrocopy	retro_nleu_2993,
Oryctolagus cuniculus	ENSOCUG00000015808	2 retrocopies	retro_ocun_112, retro_ocun_160,
Otolemur garnettii	ENSOGAG00000008408	1 retrocopy	retro_ogar_151,
Pongo abelii	ENSPPYG00000012334	1 retrocopy	retro_pabe_209,
Pan troglodytes	ENSPTRG00000012021	1 retrocopy	retro_ptro_2314,
Pteropus vampyrus	ENSPVAG00000001242	3 retrocopies	retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus	ENSSARG00000004651	1 retrocopy	retro_sara_425,
Sus scrofa	ENSSSCG00000008335	1 retrocopy	retro_sscr_62,
Ictidomys tridecemlineatus	ENSSTOG00000000714	1 retrocopy	retro_itri_59,
Tursiops truncatus	ENSTTRG00000007493	3 retrocopies	retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos	ENSVPAG00000001756	1 retrocopy	retro_vpac_617,