RetrogeneDB ID: retro_chof_2057

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_46939:4928..5966(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSCHOG00000003210
• Aliases: None
• Description: nucleosome assembly protein 1-like 1 [Source:HGNC Symbol;Acc:7637]

Sequence

>retro_chof_2057
ATGGCAGACATTGACAACAAAGAACAGTCTGAACTTGATCAAGATTTGGATGATGTTGAAGAAGTAGAAGAAGAAGAAAC
TGGTGAAGAAACAAAAATCAAAGCACGTCAGCTGACTGTTCAAATGATGCAAAATCCTCAGATTCTTGCAGCCCTTCAAG
AAAGACTTGATGGTCTGGTAGAAACACCAACAGGATACATTGAAAGCTTGCCTAGGGTAGTTAAAAGACGAGTGAATGCC
CTCAAAAACCTTCAACCTAATTGTGCAAAGATAAAAGCCAAATTTCATGAGGAAGTTCGTGATCTTGAAAGGAAGTATGC
TGTTCTCTATCAGCCACTATTTGATAAGCAATTTGAGATCATCAGTACAGTTTATGAACCTACAGAAGAAGAATGTGAAT
GGAAACCAGATGAGGAAGATGAAATTTCGGAGGAGCTGAAAGAAAAGGCCAAGATAGAAGAAGAGAAAAAGGATGAAGAA
AAAGAAGACCCCAAAGGAATTCCTGAATTTTGGTTGACTGTTTTTAAGAATGTTGACTTGCTCAGTGATATGGTTCAGGA
ACATGATGAACCTATTCTGAAGCACTTGAAGGATATTAAAGTGAAGTTCTCCGATGCTGGTCAGCCTATGAGTTTTGTCT
TAGAATTTCACTTTGAACCCAATGAGTATTTCACAAATGAAGTGTTGACAAAGACATATAGGATGAGGTCAGAACCAGAT
GATTCTGATCCCTTTTCTTTTGATGGACCAGAAATTATGGGTTGTACAGGGTGTCAGATAGATTGGAAAAAAGGAAAGAA
TGTCACTTTGAAAACCATTAAAAAGAAGCAGAAACACAAGGGACGTGGGACAGTTCGTACTGTGACTAAAACTGTCTCCA
ATGACTCTTTCTTTAATTTTTTTGCTCCTCCTGAAGTTCCTGAGAGTGGAGATCTGGATGATGATGCTGAAGCTATCCTT
GCTGCAGACTTTGAGATTGGCCACTTTTTACGTGAGCGTATAATCCCAAGATCAGTGTTATACTTTACTGGAGAAGCT

Alignment

ORF - retro_chof_2057 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.71 %
• Parental protein coverage: 88.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADIDXXXXXXXDQ---DLDDVEE--TGEETK-KARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
          MADID.......DQ...D...VEE..TGEETK.KARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
Retrocopy MADIDNKEQSELDQDLDDVEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL

Parental  PRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRFEIINAIYEPTEEECEWKPDEED
          PRVVKRRVNALKNLQ..CA.I.AKF.EEV.DLERKYAVLYQPLFDK.FEII...YEPTEEECEWKPDEED
Retrocopy PRVVKRRVNALKNLQPNCAKIKAKFHEEVRDLERKYAVLYQPLFDKQFEIISTVYEPTEEECEWKPDEED

Parental  EISEELKEKAKIEEEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDITVKFSDAGQPM
          EISEE..................PKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDI.VKFSDAGQPM
Retrocopy EISEEXXXXXXXXXXXXXXXXXXPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPM

Parental  SFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCT-CQIDWKKGKNVTLKTIKKKQKHK
          SFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCT.CQIDWKKGKNVTLKTIKKKQKHK
Retrocopy SFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQKHK

Parental  GRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDDAEAILAADFEIGHFLRERIIPRSVLYFTGEA
          GRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDDAEAILAADFEIGHFLRERIIPRSVLYFTGEA
Retrocopy GRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDDAEAILAADFEIGHFLRERIIPRSVLYFTGEA

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_2057 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 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Choloepus hoffmanni	ENSCHOG00000003210	2 retrocopies	retro_chof_1095, retro_chof_2057 ,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Pongo abelii	ENSPPYG00000004786	2 retrocopies	retro_pabe_2287, retro_pabe_999,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,