RetrogeneDB ID: retro_chof_2124

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_51349:1992..2857(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000005146
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VPS37A
• Ensembl ID: ENSCHOG00000000682
• Aliases: None
• Description: vacuolar protein sorting 37 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:24928]

Sequence

>retro_chof_2124
AATTCAGATCTTGGAAAAATTATTCAAAGTCTATTGGATGAGTTTTGGAAGAATCCTCCAGTTTTGGCTCCCACTTCAAC
AGCATTTCCATACCTATATAGTAACCCAGATGGGATGCCTCCTTATGCTTCTCAGGGTTTTTCATATCTTCCTCCATACC
CCCCACAAGAAGCTAACAGGACCATCACCTCTGTATCTGTTGCTGACACTGTTTCTTCAACCTCAAGTTATACCACAGCC
AAACCCACTGCTCCTTCATTTGGTTTCCTTTCAAATCTGCCGTTACCTGTTCCCACAACAGACATTTCTGCACCGGTAAG
CCAAAATGGTTTTGGATACAAGATGCCAGATGTCCCTGATACATTTCCAGAACTCCCAGAACTAAGTGTGTCACAACTCA
CAGATATGAATGAACAGGAGGAGATATTACTAGAACAGTTTCTTACTTTACCTCAACTAAAACAAATTATTAATGACAAG
GATGACTTAGTAAAGAGTATTGAGGAGCTGGCAAGAAAAAAACCTCCTTTTGGAGCCCAGCTTGGAAGCCAAAAGGCAGA
CTGTTTTAGATAAGTATGAATTACTTTCACAAATGAAATCTACTTTTGAAAAGAAGATGCAAAGGCAGCATGAACTTAGT
GAGAGCTGTAGTGCAAGTGCCCTACAGGCAAGATTAAAAGTAGCTGCACATGAATCTGAGGAAGAATCTGATAATATTGC
TGAAGATTTCTTGGAAGGAAAAACTGAAATAGATGATTTTCTTAGTAGCTTCATGGAAAAGAGAACAATTTGCCACTGTA
GAAGAGCCAAGGAAGAGAAACTTCAACAGGCAATAGCAATGCACATCCAGTTTCATGCTCCACTA

Alignment

ORF - retro_chof_2124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.19 %
• Parental protein coverage: 72.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HSDLGKIIQSLLDEFWKNPPVLAPTSTAFPYIYSNPGGMPPYAYQGFSYLPPYPPQEANRTITSVSVADT
          .SDLGKIIQSLLDEFWKNPPVLAPTSTAFPY.YSNP.GMPPYA.QGFSYLPPYPPQEANRTITSVSVADT
Retrocopy NSDLGKIIQSLLDEFWKNPPVLAPTSTAFPYLYSNPDGMPPYASQGFSYLPPYPPQEANRTITSVSVADT

Parental  VSSTSSYTTAKPAAPSFGFLSNLPLPVPTTDTSAPVSQNGFGYKMPDVPDTFPELSELSVSQLTDMNEQE
          VSSTSSYTTAKP.APSFGFLSNLPLPVPTTD.SAPVSQNGFGYKMPDVPDTFPEL.ELSVSQLTDMNEQE
Retrocopy VSSTSSYTTAKPTAPSFGFLSNLPLPVPTTDISAPVSQNGFGYKMPDVPDTFPELPELSVSQLTDMNEQE

Parental  EILLEQFLTLPQLKQIINDKDDLVKSIEELARK-NLLLEPSLEAKRQTVLDKYELLSQMKSTFEKKMQRQ
          EILLEQFLTLPQLKQIINDKDDLVKSIEELARK.NLLLEPSLEAKRQTVLDKYELLSQMKSTFEKKMQRQ
Retrocopy EILLEQFLTLPQLKQIINDKDDLVKSIEELARK>NLLLEPSLEAKRQTVLDKYELLSQMKSTFEKKMQRQ

Parental  HELSESCSASALQARLKVAAHEAEEESDNIAEDFLEGKT-IDDFLSSFMEKRTICHCRRAKEEKLQQAIA
          HELSESCSASALQARLKVAAHE.EEESDNIAEDFLEGKT.IDDFLSSFMEKRTICHCRRAKEEKLQQAIA
Retrocopy HELSESCSASALQARLKVAAHESEEESDNIAEDFLEGKTEIDDFLSSFMEKRTICHCRRAKEEKLQQAIA

Parental  MHSQFHAPL
          MH.QFHAPL
Retrocopy MHIQFHAPL

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_2124 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 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000682	2 retrocopies	retro_chof_1257, retro_chof_2124 ,
Callithrix jacchus	ENSCJAG00000011769	1 retrocopy	retro_cjac_1790,
Dipodomys ordii	ENSDORG00000014879	9 retrocopies	retro_dord_257, retro_dord_294, retro_dord_542, retro_dord_544, retro_dord_580, retro_dord_598, retro_dord_631, retro_dord_668, retro_dord_751,
Homo sapiens	ENSG00000155975	1 retrocopy	retro_hsap_3256,
Gorilla gorilla	ENSGGOG00000011650	1 retrocopy	retro_ggor_2217,
Nomascus leucogenys	ENSNLEG00000002558	1 retrocopy	retro_nleu_2687,
Pongo abelii	ENSPPYG00000018386	2 retrocopies	retro_pabe_2699, retro_pabe_2821,
Pan troglodytes	ENSPTRG00000020019	1 retrocopy	retro_ptro_2202,