RetrogeneDB ID: retro_chof_467

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_112552:2361..2925(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GGCT
• Ensembl ID: ENSCHOG00000008757
• Aliases: None
• Description: gamma-glutamylcyclotransferase [Source:HGNC Symbol;Acc:21705]

Sequence

>retro_chof_467
ATGGCGAGCTCGGGCTGTGGGAACTGCCCAGGAAACGAGGAGGAGAGTTTTCTGTACTTTGCCTACCGCAGCATCCTGTT
CACGGAGAGAATCTGCCTCCGAAACCCCTCGGCTGCCTTCTGCAGCGTGGCCTGCCTGCAGGATTTTAAGCTCGACTTTG
GCAATTCCCAAGGCAAAATAACTCATACTTGACATGGACGAATAACTACCATTTTTCAAAGTCCTGGAGATGAAGTGTGG
GGAGTAGTACGGAAAATGAACAAAAGCAGTTTATGTTCTCTGGATGAGCAAGAAGGGATTGTAAGTGGAACATATGATCC
AATAGAAGTTAATGTTCACACTCAAGAAGGAGAGAAAATAACCTGTCGAAGTTATCAGATGAAAAATTATGTGAGTGTTC
CCCCATCACCACAGTATAAAAAGGTCATTTGCATGGGTGCAAAAGAGAATGGTTTACCACTGGAATATCAAAAGAAGTTA
AAAGCAATAGAACCAAATGACTATAAAGGAAAGGTCTCAGAAGAAATTGAAGATATTATCAAAAAGGGGGAAACAAAATC
TCAT

Alignment

ORF - retro_chof_467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASPGCGNCPGNEEESFLYFAYGSNLLTERIHLRNPSAVFCSVARLQDFKLDFGNSQGKISHTWHGGIAT
          MAS.GCGNCPGNEEESFLYFAY.S.L.TERI.LRNPSA.FCSVA.LQDFKLDFGNSQGKI.HT.HG.I.T
Retrocopy MASSGCGNCPGNEEESFLYFAYRSILFTERICLRNPSAAFCSVACLQDFKLDFGNSQGKITHT*HGRITT

Parental  IFQSPGDEVWGVVWKMNKSNLCSLDEQEGVVSGTYDPIEVNVHTQEGEEITCRSYQMKNYVSAAPSPQYK
          IFQSPGDEVWGVV.KMNKS.LCSLDEQEG.VSGTYDPIEVNVHTQEGE.ITCRSYQMKNYVS..PSPQYK
Retrocopy IFQSPGDEVWGVVRKMNKSSLCSLDEQEGIVSGTYDPIEVNVHTQEGEKITCRSYQMKNYVSVPPSPQYK

Parental  KVICMGAKENGLPLEYQKKLKAIEPSDYKGRVSEEIEDIIKKGETKSH
          KVICMGAKENGLPLEYQKKLKAIEP.DYKG.VSEEIEDIIKKGETKSH
Retrocopy KVICMGAKENGLPLEYQKKLKAIEPNDYKGKVSEEIEDIIKKGETKSH

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_467 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008757	1 retrocopy	retro_chof_467 ,
Callithrix jacchus	ENSCJAG00000008589	1 retrocopy	retro_cjac_1211,
Dasypus novemcinctus	ENSDNOG00000007242	1 retrocopy	retro_dnov_2324,
Mustela putorius furo	ENSMPUG00000005083	1 retrocopy	retro_mputfur_1157,
Otolemur garnettii	ENSOGAG00000013316	1 retrocopy	retro_ogar_2457,
Ochotona princeps	ENSOPRG00000005329	2 retrocopies	retro_opri_170, retro_opri_505,