RetrogeneDB ID: retro_chof_1873

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_41046:2853..5321(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000001946
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSPH1
• Ensembl ID: ENSCHOG00000013998
• Aliases: None
• Description: heat shock 105kDa/110kDa protein 1 [Source:HGNC Symbol;Acc:16969]

Sequence

>retro_chof_1873
TCAGTCATATCATTTGGATCAAAAAACAGAACAATTGGAGTTGCAGCAAAAAATCAGCAAATCACTCATGCAAACAACAC
AGTATCTAACTTCAAGAGATTTCATGGCCGAGCATTCAGTGACCCCTTCATTCAAAAAGAGAAGGAAAACTTAAGCTACG
ATTTGGTTCCGATGAAAAATGGTGGAGTTGGAATAAAGGTAATGTACATGGATGAAGAACATCTGTTTAGTGTGGAACAG
ATAACAGCCATGTTGTTGACTAAGTTAAAGGAAACTGCTGAAAACAACCTCAAGAAGCCAGTGACAGATTGTGTTATTTC
AGTGCCCTCCTTCTTCACGGATGCGGAGAGGCGATCTGTGTTGGATGCTGCACAGATTGTTGGCCTAAACTGCTTGAGAC
TTATGAATGACATGACTGCTGTTGCTTTGAATTATGGAATTTATAAGCAGGATCTCCCCGGCCTGGATGAGAAACCTCGG
ATAGTGGTTTTTGTTGATATGGGACATTCAGCTTTTCAAGTGTCTGCCTGTGCCTTTAACAAGGGAAAATTGAAGGTATT
GGGAACTGCTTTTGATCCTTTCTTGGGAGGAAAGAACTTTGATGAAAAGTTAGTGGAACATTTTTGTGCAGAATTTAAGA
CCAAGTACAAGTTGGATGCAAAATCCAAAATTCGAGCACTCCTTCGTCTGTATCAGGAGTGTGAAAAGTTGAAAAAGCTA
ATGAGCTCGAACAGCACAGACCTGCCATTGAATATCGAGTGCTTTATGAATGACAAAGATGTTTCGGGAAAGATGAACAG
GTCACAATTTGAAGAACTCTGTGCTGACCTGCTGCAAAAAATAGAAATACCCCTTTATTCGCTGATGGAACAAACTCGAC
TAAAAGTAGAAGATGTGAGTGCTGTTGAGATCGTTGGAGGCACTACACGAATTCCAGCTGTGAAAGAAAGAATTGCCAAG
TTCTTCGGAAAAGACATCAGCACAACCCTTAACGCAGATGAAGCCGTAGCCAGAGGATGTGCGCTGCAGTGTGCAGCTCT
TTCCCCGGCTTTTAAAGTTAGGGAGTTTTCTGTCACAGATGCAATTCCTTTTCCGATATCGCTGATCTGGAATCACGATT
CAGAAGATACTGAAGGTGTTCATGAAGTGTTCAGCCGCAACCATGCTGCACCTTTCTCCAAAGTTCTCACCTTCTACAGA
AGGGGGCCTTTTGAGCTAGAAGCTTTCTATTCTGATCCTCAAGGAGTTCCATATCCAGAAGCAAAAATAGGCTGCTTCAT
AGTTCAGAATGTTTCTGCCCAGAAAGATGGAGAAAAATCTAAGGTGAAAGTTAAAGTGCGGGTCAACACCCATGGCATTT
TCACCATCTCTACAGCATCTATGGTGGAGAAGATCCCAACTGAGGAAAATGAAGGGTCATCTCTTGAAGCAGACATGGAG
TGTGCTAATCAGAGACCACCAGAAAACCCCGACAGTGATAAAAATATCCAGCAAGACAACAGTGAAGCTGGAACACAGCC
CCAGGTACAAACTGATGCTCAACAAACCTCACAGTCTCCCCCTTCATCTGAACTTACCTCAGAAGAAAACAAAATCCCAG
ATGCTGACAAAGCCAATGAAAAGAAGGTTGACCAGCCTCCAGAAGCTAAAAAACCCAAAATAAAGGTGGTGAACGTTGAG
CTGCCTATTGAAGCCAATTTGGTCTGGCAGTTAGGGAAAGACCTTCTTAACATGTATATTGAGACAGAGGGTAAGATGAT
AATGCAGGATAAATTGGAAAAGGAAAGAAATGACGCTAAAAATGCGGTGGAAGAGTATGTGTATGAGTTCAGGGACAAGC
TCTGTGGACCATATGAAAAATTCATAAGTGAACAGGATCCTCAGCATTTCCTGAGGCTCTTCTCTTTTTCTGAAGACTGG
CTCTATGAAGAAGGAGAGGACCAAGCCAAACAGGCATATGTGACAAGCTGGAAGAGTTAACGAAAATTGGCACTCCAATT
AAAATCCGGTTTCAAGAGGCTGAGGACCGGCCAAAACTGTTTGAAGAGCTGGGGCAGAGGCTCCAGCACTACGCCAAGAT
AGCAGCTGACTTCAGAAACCAGGATGAGAAGTATAACCATATCGATGAGTCTGAAATGAAGAAGGTTGAGAAGTCTGTCA
ATGAAGTGATGGAGTGGATGAACAACATCATAAATGTGCAGGCTAAAAGGAGCCTGGAGCAGGACCCTGTTGTCCAAGCA
CAGGAAATTAAAGCAAAATTGAAGGAACTGAACAACACTTGTGAACCAATTGTAACACAACCCAAGCCAAAAATCGAGTC
ACCCAAACTGGAGAGAACTCCAAATGGCCCAAATGTTGATAAGAAGGAAGAAGATTTAGAAGGCAAGAATGATTTTGGTG
CTGAGCCGCCACATCAGAATGGTGACTGCTACCCAAACGAGAAGAACTCCGCCCACATGGACTTGGAC

Alignment

ORF - retro_chof_1873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVISFGSKNRTIGVAAKNQQITHANNTVSNFKRFHGRAFSDPFIQKEKENLSYDLVPMKNGGVGIKVMYM
          SVISFGSKNRTIGVAAKNQQITHANNTVSNFKRFHGRAFSDPFIQKEKENLSYDLVPMKNGGVGIKVMYM
Retrocopy SVISFGSKNRTIGVAAKNQQITHANNTVSNFKRFHGRAFSDPFIQKEKENLSYDLVPMKNGGVGIKVMYM

Parental  DEEHLFSVEQITAMLLTKLKETAENNLKKPVTDCVISVPSFFTDAERRSVLDAAQIVGLNCLRLMNDMTA
          DEEHLFSVEQITAMLLTKLKETAENNLKKPVTDCVISVPSFFTDAERRSVLDAAQIVGLNCLRLMNDMTA
Retrocopy DEEHLFSVEQITAMLLTKLKETAENNLKKPVTDCVISVPSFFTDAERRSVLDAAQIVGLNCLRLMNDMTA

Parental  VALNYGIYKQDLPGLDEKPRIVVFVDMGHSAFQVSACAFNKGKLKVLGTAFDPFLGGKNFDEKLVEHFCA
          VALNYGIYKQDLPGLDEKPRIVVFVDMGHSAFQVSACAFNKGKLKVLGTAFDPFLGGKNFDEKLVEHFCA
Retrocopy VALNYGIYKQDLPGLDEKPRIVVFVDMGHSAFQVSACAFNKGKLKVLGTAFDPFLGGKNFDEKLVEHFCA

Parental  EFKTKYKLDAKSKIRALLRLYQECEKLKKLMSSNSTDLPLNIECFMNDKDVSGKMNRSQFEELCADLLQK
          EFKTKYKLDAKSKIRALLRLYQECEKLKKLMSSNSTDLPLNIECFMNDKDVSGKMNRSQFEELCADLLQK
Retrocopy EFKTKYKLDAKSKIRALLRLYQECEKLKKLMSSNSTDLPLNIECFMNDKDVSGKMNRSQFEELCADLLQK

Parental  IEIPLYSLMEQTRLKVEDVSAVEIVGGTTRIPAVKERIAKFFGKDISTTLNADEAVARGCALQCAALSPA
          IEIPLYSLMEQTRLKVEDVSAVEIVGGTTRIPAVKERIAKFFGKDISTTLNADEAVARGCALQCAALSPA
Retrocopy IEIPLYSLMEQTRLKVEDVSAVEIVGGTTRIPAVKERIAKFFGKDISTTLNADEAVARGCALQCAALSPA

Parental  FKVREFSVTDAIPFPISLIWNHDSEDTEGVHEVFSRNHAAPFSKVLTFYRRGPFELEAFYSDPQGVPYPE
          FKVREFSVTDAIPFPISLIWNHDSEDTEGVHEVFSRNHAAPFSKVLTFYRRGPFELEAFYSDPQGVPYPE
Retrocopy FKVREFSVTDAIPFPISLIWNHDSEDTEGVHEVFSRNHAAPFSKVLTFYRRGPFELEAFYSDPQGVPYPE

Parental  AKIGRFIVQNVSAQKDGEKSKVKVKVRVNTHGIFTISTASMVEKIPTEENEGSSLEADMECANQRPPENP
          AKIG.FIVQNVSAQKDGEKSKVKVKVRVNTHGIFTISTASMVEKIPTEENEGSSLEADMECANQRPPENP
Retrocopy AKIGCFIVQNVSAQKDGEKSKVKVKVRVNTHGIFTISTASMVEKIPTEENEGSSLEADMECANQRPPENP

Parental  DSDKNIQQDNSEAGTQPQVQTDAQQTSQSPPSSELTSEENKIPDADKANEKKVDQPPEAKKPKIKVVNVE
          DSDKNIQQDNSEAGTQPQVQTDAQQTSQSPPSSELTSEENKIPDADKANEKKVDQPPEAKKPKIKVVNVE
Retrocopy DSDKNIQQDNSEAGTQPQVQTDAQQTSQSPPSSELTSEENKIPDADKANEKKVDQPPEAKKPKIKVVNVE

Parental  LPIEANLVWQLGKDLLNMYIETEGKMIMQDKLEKERNDAKNAVEEYVYEFRDKLCGPYEKFISEQDHQHF
          LPIEANLVWQLGKDLLNMYIETEGKMIMQDKLEKERNDAKNAVEEYVYEFRDKLCGPYEKFISEQD.QHF
Retrocopy LPIEANLVWQLGKDLLNMYIETEGKMIMQDKLEKERNDAKNAVEEYVYEFRDKLCGPYEKFISEQDPQHF

Parental  LRLLTETEDWLYEEGEDQAKQAYV-DKLEELTKIGTPIKIRFQEAEDRPKLFEELGQRLQHYAKIAADFR
          LRL....EDWLYEEGEDQAKQAYV.DKLEELTKIGTPIKIRFQEAEDRPKLFEELGQRLQHYAKIAADFR
Retrocopy LRLFSFSEDWLYEEGEDQAKQAYV<DKLEELTKIGTPIKIRFQEAEDRPKLFEELGQRLQHYAKIAADFR

Parental  NQDEKYNHIDESEMKKVEKSVNEVMEWMNNIINVQAKRSLEQDPVVQAQEIKAKLKELNNTCEPIVTQPK
          NQDEKYNHIDESEMKKVEKSVNEVMEWMNNIINVQAKRSLEQDPVVQAQEIKAKLKELNNTCEPIVTQPK
Retrocopy NQDEKYNHIDESEMKKVEKSVNEVMEWMNNIINVQAKRSLEQDPVVQAQEIKAKLKELNNTCEPIVTQPK

Parental  PKIESPKLERTPNGPNVDKKEEDLEGKNDFGAEPPHQNGDCYPNEKNSAHMDLD
          PKIESPKLERTPNGPNVD............GAEPPHQNGDCYPNEKNSAHMDLD
Retrocopy PKIESPKLERTPNGPNVDXXXXXXXXXXXXGAEPPHQNGDCYPNEKNSAHMDLD

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_1873 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004852	1 retrocopy	retro_chof_589,
Choloepus hoffmanni	ENSCHOG00000013998	1 retrocopy	retro_chof_1873 ,
Monodelphis domestica	ENSMODG00000009347	1 retrocopy	retro_mdom_1049,