RetrogeneDB ID: retro_chof_1257

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_239001:801..1864(+)
• Located in intron of: None

Retrocopy information

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

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_1257
ATAGCTGAAATACAGAAAGATGTGGAGTACAGATTACCATTCACTGTAAACAACCTGACAATTAACATTAATATATTGCT
TCCTCCACAATTTCCTCAGGAAAAACCAATGATCAGTGTTTATCCACCAATACGGCATCACTTAATGGATAAACAAGGAG
TGTATGTTACCTGTCCATTAGTAAACAATTTTACAATGCACTCAGATCTTGGAAAAATTATTCAAAGTCTATTGGATGAG
TTTTGGAAGAATCCTCCAGTTTTGGCTCCCACTTCAACAGCATTTCCATACCTATATAGTAACCCAGGTGGGATGCCTCC
TTATGCTTCTCAGGGTTTTTCATATCTTCCTCCATACCCCCCACAAGAAGCTAACAGGACCATCACCTCTGTATCTGTTG
CTGACACTGTTTCTTCAACCTCAAGTTACACCACAGCCAAACCCGCTGCTCCTTCATTTGGTTTCCTTTCAAATCTGCCG
TTACCTGTTCCCACAACAGACACTTCTGCACCGGTAAGTCAAAATGGTTTTGGATACAAGATGCCAGATGTCCCTGATAC
ATTTCCAGAACTCCCAGAACTAAGTGTGTCACAACTCACAGATATGAATGAACAGGAGGAGATATTACTAGAACAGTTTT
CTTACTTTACCTCAACTAAAACAAATTATTAATGACAAGGATGACTTAGTAAAGAGTATTGAGGAGCTGGCAAGAAAAAA
TCTCCTTTTGGAGCCCAACTTGGAAGCCAAAAGGCAGACTGTTTTAGATAAGTATGAATTACTTTCACAAATGAAATCTA
CTTTTGAAAAGAAGATGCAAAGGCAGCATGAACTGAGTGAGAGCTGTAGTGCAAGTGCCCTACAGGCAAGATTAAAAGTA
GCTGCACATGAAGCTGAGGAAGAATCTGATAATATTGCTGAAGATTTCTTGGAAGGAAAAACTGAAATAGATGATTTTCT
TAGTAGCTTCATGGAAAAGAGAACAATTTGCCACTGTAGAAGAGCCAAGGAAGAGAAACTTCAACAAGCAATAGCTATGC
ACAGCCAGTTTCATGCTCCACTA

Alignment

ORF - retro_chof_1257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.03 %
• Parental protein coverage: 89.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IAEIQKDVEYRLPFTVNNLTININILLPPQFPQEKPVISVYPPIRHHLMDKQGVYVTCPLVNNFTMHSDL
          IAEIQKDVEYRLPFTVNNLTININILLPPQFPQEKP.ISVYPPIRHHLMDKQGVYVTCPLVNNFTMHSDL
Retrocopy IAEIQKDVEYRLPFTVNNLTININILLPPQFPQEKPMISVYPPIRHHLMDKQGVYVTCPLVNNFTMHSDL

Parental  GKIIQSLLDEFWKNPPVLAPTSTAFPYIYSNPGGMPPYAYQGFSYLPPYPPQEANRTITSVSVADTVSST
          GKIIQSLLDEFWKNPPVLAPTSTAFPY.YSNPGGMPPYA.QGFSYLPPYPPQEANRTITSVSVADTVSST
Retrocopy GKIIQSLLDEFWKNPPVLAPTSTAFPYLYSNPGGMPPYASQGFSYLPPYPPQEANRTITSVSVADTVSST

Parental  SSYTTAKPAAPSFGFLSNLPLPVPTTDTSAPVSQNGFGYKMPDVPDTFPELSELSVSQLTDMNEQEEILL
          SSYTTAKPAAPSFGFLSNLPLPVPTTDTSAPVSQNGFGYKMPDVPDTFPEL.ELSVSQLTDMNEQEEILL
Retrocopy SSYTTAKPAAPSFGFLSNLPLPVPTTDTSAPVSQNGFGYKMPDVPDTFPELPELSVSQLTDMNEQEEILL

Parental  EQ-FLTLPQLKQIINDKDDLVKSIEELARKNLLLEPSLEAKRQTVLDKYELLSQMKSTFEKKMQRQHELS
          EQ.FLTLPQLKQIINDKDDLVKSIEELARKNLLLEP.LEAKRQTVLDKYELLSQMKSTFEKKMQRQHELS
Retrocopy EQ>FLTLPQLKQIINDKDDLVKSIEELARKNLLLEPNLEAKRQTVLDKYELLSQMKSTFEKKMQRQHELS

Parental  ESCSASALQARLKVAAHEAEEESDNIAEDFLEGKT-IDDFLSSFMEKRTICHCRRAKEEKLQQAIAMHSQ
          ESCSASALQARLKVAAHEAEEESDNIAEDFLEGKT.IDDFLSSFMEKRTICHCRRAKEEKLQQAIAMHSQ
Retrocopy ESCSASALQARLKVAAHEAEEESDNIAEDFLEGKTEIDDFLSSFMEKRTICHCRRAKEEKLQQAIAMHSQ

Parental  FHAPL
          FHAPL
Retrocopy FHAPL

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_1257 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,