RetrogeneDB ID: retro_chof_2560

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_86314:4396..6623(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NASP
• Ensembl ID: ENSCHOG00000010436
• Aliases: None
• Description: nuclear autoantigenic sperm protein (histone-binding) [Source:HGNC Symbol;Acc:7644]

Sequence

>retro_chof_2560
AATGTGGATAGTGAAGCTAAGAAACTATTGGGTTTAGGACAGAAACACCTCGTGATGGGGGATATTCCAGCAGCTGTCAA
TGCATTCCAGGAAGCAGCTAGTCTTTTAGGTAAGAAGTATGGAGAAACAGCTAATGAGTGTGGAGAAGCCTTCTTTTTCT
ATGGGAAATCGCTTCTGGAGTTGGCAAGAATGGAGAATGGTGTGTTGGGAAATGCCCTGGAAGGTGTGCATGTGGAAGAG
GAGGAAGGAGAAAAAACAGAAGACGAGTCTCTGGCAGAAAATAATGATAATATAGATGAGGAAGCAAGGGAAGAGTTGAG
AGAACAGGTTTATGACGCCATGGGAGAAAAAAGAAGAAGCCCAAAAAACAGAAGACAAGTCTCTTGTAAAGCCTGAAACT
GATAAAGAACAGGAGCTTGAAATGGAGAAGGGTGGAAGAGAAGATATGGATATAACTGAGCTTACAGAGGAGCAACAGGA
AAAAGTTCAGTCACCACCAGATCAGCTAATTGAAACCGCTGAAGAGGCAAAAGGAGCAGCAGCACCAGAAGGACTGAACG
AAGCTGAAGTCAATTCTGGGAAGCCAGAACAGGAAGTACCAGATACTGAGGAAGGAAAAGCAGTATCTGGAATAGATATC
CAAGAAGAAGAGTGCAGAGAAAAAGGTCAGGAGAAACAGGGAGAGGTATTTGTGAGCATAGAGGAAGAACCAAAAGAAGC
TTCAGAAGAGCAGCCTGCTGTGACTCTAGAAGAGCAGGGCACTGCAGTGGAGGTAGAAGCAGAACCTATAGACCCAACGG
TCAAGCCGGTGCCTGTGGGTGGGGAGGAACCAAATGAGCAGGTAGCTACCTCTGATAAAGAACCAGGGAAGGCTCTTCTT
GAGGAGCAGCTGATAGTGCAAGAAGTGCCACTTGCTGAAGAGTCACCACAGGTGACACCAGAGGCTGCAGAGGCATTGGC
TGTGGAGGCTGGATCAGGAGACTCTGAGAAGCCCAGACAGGAGGCCACAGTCAATGGACTGTCCACTGCAGGAGACCAGA
CTCCTATTGAACCACAGACAACTTCTGCAGAAGGACTGACAGAAACAAAAGATGGCTCTGGAGTAGAGGAGAAGGTCAGG
GCAGAGCTGGTTCCTAGCCAAGAGACTCAGCTGTTCATAGAAGAGTCTGAGGCAGCTGGAGATGGGGTTGAGACCAAGGT
AGTCAAGGAGGCTACTGAGAAACCACCTGAAGACAAAGTTAAGATAGCTGCTAATGAAGAGACACAAGAGAAAGAAGAAC
AGATGAAAGAGGGTGAAGAAACTGAAGGCTCAGAAGAGGAGGATAAAGAAAATGACAAGGCTGAAGAAATACCAAATGAT
TCCGTTGTTGACAATAAGTCTCTTCAAGAAAATGAAGAGGAGGAAATTGGGAACCTAGAGCTTGCCTGGGATATGCTGGA
TTTAGCGAAGATCATTTTTAAAAGACAAGAAACAAAAGAAGCTCAGCTTTATGCTGCACAGGCACATCTTAAACTTGGAG
AAGTTAGTGTTGAATCAGAGAATTATGTCCAAGCTGTGAAGGAGTTCCAGGCTTGCTTAAACCTGCAAGAGCAGTACCTA
GAAGCCCACGACTGTCTCCTTGCAGAGACCCACTACCAGCTGGGCTTGGCCTATGGGTACAACTCCCAGTATGATGAGGC
AGTGGCACAATTCAGCAAATCTATTGAAGTCATTGAGAAGAGAATGGCTGTACTAAATGAGCAGATGAAGGAGGCTGAAG
GATCAACTACTGAATATGAGAAAGAAATTGAGGAGCTGAAGGAACTGCTACCCGAAATTAAAGAGAAGATAGAAGACACA
AAGGAGTCCCAGCGCAGTGGCAATGTAGCTGAATTGGCTCTGAAAGCTACTCTGGTGGAAAGCTCTACCTCGGGTTTCAC
TTCTAGCGGAGGAAGCTCTTCAGTCTCCATGATTGCCAGTAGAAAGCCAACAGATGGTGCTTCCTCGTCAAACTGTGTGA
CTGATATTTCTCATCTTGTCAGAAAGAAGAGGAAACCAGAGGAAGAGAGCCCCCAGAAAGATGATGCAAAGAAAGCCAAA
CAAGAACCAGAGGTGAATGGAGGCAGTGGGGATGCTGTCCCCAGTGGAAATGAAGTTTTCGAACACATGGAGGAGGAGGC
TGAGAATCAGGCTGAAAGCCGGGCAGCAGTGGAGGGGACAATGGAGGCCGGAGCTACAGTTGAAAGC

Alignment

ORF - retro_chof_2560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.23 %
• Parental protein coverage: 94.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DVDSEAKKLLGLGQKHLVMGDIPAAVNAFQETASLLGKKYGETANECGEAFFFYGKSLLELARMENGVLG
          .VDSEAKKLLGLGQKHLVMGDIPAAVNAFQE.ASLLGKKYGETANECGEAFFFYGKSLLELARMENGVLG
Retrocopy NVDSEAKKLLGLGQKHLVMGDIPAAVNAFQEAASLLGKKYGETANECGEAFFFYGKSLLELARMENGVLG

Parental  NALQGVHVEEEEGEKTEDESLVENNDNLDEEAREELREQVYDAMGEK-EEAQKTEDKSLVKPETDKEQEL
          NAL.GVHVEEEEGEKTEDESL.ENNDN.DEEAREELREQVYDAMGEK.EEAQKTEDKSLVKPETDKEQEL
Retrocopy NALEGVHVEEEEGEKTEDESLAENNDNIDEEAREELREQVYDAMGEK>EEAQKTEDKSLVKPETDKEQEL

Parental  EMEKGGREDMDISELTEEQQEKVQSPPDQLIETTEEAKGAAAPEGLNEAEVNSGKPEQEVPDTEEGKAVS
          EMEKGGREDMDI.ELTEEQQEKVQSPPDQLIET.EEAKGAAAPEGLNEAEVNSGKPEQEVPDTEEGKAVS
Retrocopy EMEKGGREDMDITELTEEQQEKVQSPPDQLIETAEEAKGAAAPEGLNEAEVNSGKPEQEVPDTEEGKAVS

Parental  GIDIQEE-CREKGQEKQGEVFVSIEEKPKEASEEQPAVTLEEQGTAVEVEAEPIDPTVKPVPVGGEEPNE
          GIDIQEE.CREKGQEKQGEVFVSIEE.PKEASEEQPAVTLEEQGTAVEVEAEPIDPTVKPVPVGGEEPNE
Retrocopy GIDIQEEECREKGQEKQGEVFVSIEEEPKEASEEQPAVTLEEQGTAVEVEAEPIDPTVKPVPVGGEEPNE

Parental  QVATSDKEPGKALLEEQLIVQEVPLAEESPQVTPEASEALAVEAGSGDSEKPRQEATVNGLSTAGDQTPI
          QVATSDKEPGKALLEEQLIVQEVPLAEESPQVTPEA.EALAVEAGSGDSEKPRQEATVNGLSTAGDQTPI
Retrocopy QVATSDKEPGKALLEEQLIVQEVPLAEESPQVTPEAAEALAVEAGSGDSEKPRQEATVNGLSTAGDQTPI

Parental  EPQTTSAEGLTETKDGSGVEEKVRAELVPSQETQLFIEESEPAGDGVETKVVKEATEKPPEDKVKIAANE
          EPQTTSAEGLTETKDGSGVEEKVRAELVPSQETQLFIEESE.AGDGVETKVVKEATEKPPEDKVKIAANE
Retrocopy EPQTTSAEGLTETKDGSGVEEKVRAELVPSQETQLFIEESEAAGDGVETKVVKEATEKPPEDKVKIAANE

Parental  ETQEKEEQMKEGEETEGSEEEDK-NDR--EIPNDSVV-NKSLQENEEEEIGNLELAWDMLDLAKIIFKRQ
          ETQEKEEQMKEGEETEGSEEEDK.ND...EIPNDSVV.NKSLQENEEEEIGNLELAWDMLDLAKIIFKRQ
Retrocopy ETQEKEEQMKEGEETEGSEEEDKENDKAEEIPNDSVVDNKSLQENEEEEIGNLELAWDMLDLAKIIFKRQ

Parental  ETKEAQLYAAQAHLKLGEVSVESENYVQAVEEFQACLNLQEQYLEAHDRLLAETHYQLGLAYGYNSQYDE
          ETKEAQLYAAQAHLKLGEVSVESENYVQAV.EFQACLNLQEQYLEAHD.LLAETHYQLGLAYGYNSQYDE
Retrocopy ETKEAQLYAAQAHLKLGEVSVESENYVQAVKEFQACLNLQEQYLEAHDCLLAETHYQLGLAYGYNSQYDE

Parental  AVAQFSKSIEVIEKRMAVLNEQMKEAEGSTTEYEKEIEELKELLPEIKEKIEDAKESQRSGNVAELALKA
          AVAQFSKSIEVIEKRMAVLNEQMKEAEGSTTEYEKEIEELKELLPEIKEKIED.KESQRSGNVAELALKA
Retrocopy AVAQFSKSIEVIEKRMAVLNEQMKEAEGSTTEYEKEIEELKELLPEIKEKIEDTKESQRSGNVAELALKA

Parental  TLVESSTSGFTSSGGSSSVSMIASRKPTDGASSSNCVTDISHLVRKKRKPEERAPRKDDAKKAKKNPEVN
          TLVESSTSGFTSSGGSSSVSMIASRKPTDGASSSNCVTDISHLVRKKRKPEE..P.KDDAKKAK..PEVN
Retrocopy TLVESSTSGFTSSGGSSSVSMIASRKPTDGASSSNCVTDISHLVRKKRKPEEESPQKDDAKKAKQEPEVN

Parental  GGRGDAVPS-NEVSEHMEEEAENQAESRAAVEGTMEAGATVES
          GG.GDAVPS.NEV.EHMEEEAENQAESRAAVEGTMEAGATVES
Retrocopy GGSGDAVPSGNEVFEHMEEEAENQAESRAAVEGTMEAGATVES

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_2560 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010436	1 retrocopy	retro_chof_2560 ,
Homo sapiens	ENSG00000132780	1 retrocopy	retro_hsap_4064,
Macropus eugenii	ENSMEUG00000001037	1 retrocopy	retro_meug_1359,
Mus musculus	ENSMUSG00000028693	1 retrocopy	retro_mmus_1217,
Nomascus leucogenys	ENSNLEG00000014434	1 retrocopy	retro_nleu_564,
Pongo abelii	ENSPPYG00000001409	1 retrocopy	retro_pabe_3338,
Pan troglodytes	ENSPTRG00000000677	1 retrocopy	retro_ptro_2754,