RetrogeneDB ID: retro_chof_2490

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_79414:3015..3798(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAB1
• Ensembl ID: ENSCHOG00000010241
• Aliases: None
• Description: NGFI-A binding protein 1 (EGR1 binding protein 1) [Source:HGNC Symbol;Acc:7626]

Sequence

>retro_chof_2490
AAGGCTACGAGAGACTGGATTACAAACCCAGGCCTTTTCAATCAGCCTCTTACTTCCCTTCCTGTAAGTAGTATACCCAT
CTATAAAATACCAGAAGGATTACCGACATGGCTAAGAATATCTGGTAGTAGTTATGAAAGGAATAGCAGTGCCCAGGAAT
CTCATTTAAAAATCCCAAAATGTGCTGCCACCACCTGTGTGCAGAGCTTGGGACAGGGGAAATCGGATGTGGTGGGGAGT
TATAGTGCTGCAGAGTGAGTCCAGACTCTGGCAGGGCCACCATGCTACTGAGAGCAAGCACACCTCTCCCTAGCAGATCT
TGGCTCCCCAGCTTCCCCCAAGGAAAGCAGTGAAGTGCTGAATGCTGCTGCACCCTCCGTGGCCAAATGTGTGGAGCGGA
TGGCCCCCACTCTGCCAAAAAGTGACTTGAATGAAGTGAAAGAGCTGCTAAAAACCAATAAGAAGTTGGCCAAAATGATT
GGTCACATCTTTGAGATGAGTGATGATGATCCACACAAAGAGGAGGAAATTCTAAAACACAGTGCAATATATGGCAGATT
TGACTCGAAGAGAAAGGATGGGAAACATCTCACACTTCATGAGCTCACTGTTAATGAAGCAGCTGCTCAGCTCTGTGTGA
AGGATAATGCCCTGCTGACAAGAAGAGATGAACTTTTTGCCCTGGCCAGGCAGATTTCTGGAGAAGTCACCTATAAATAT
ACTTACAGAACCACTAAGTGAAAATGTGGAGAAAGAGATGAATTATCCCCGAAGAGAATTAGA

Alignment

ORF - retro_chof_2490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.85 %
• Parental protein coverage: 54.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KALRDWVTNPGLFNQPLTSLPVSSIPIYKLPEGSPTWLGISCSSYERNSSAREPHLKIPKCAATTCVQSL
          KA.RDW.TNPGLFNQPLTSLPVSSIPIYK.PEG.PTWL.IS.SSYERNSSA.E.HLKIPKCAATTCVQSL
Retrocopy KATRDWITNPGLFNQPLTSLPVSSIPIYKIPEGLPTWLRISGSSYERNSSAQESHLKIPKCAATTCVQSL

Parental  GQGKSDVAGS-LALQSVSESRLWQGHHATESEHS-LSPADLGSPASPKESSEVLDAAAALSVAECVERMA
          GQGKSDV.GS...LQS..ESRLWQGHHATES.H..LS.ADLGSPASPKESSEVL.AAA..SVA.CVERMA
Retrocopy GQGKSDVVGS>IVLQS--ESRLWQGHHATESKHT<LSLADLGSPASPKESSEVLNAAAP-SVAKCVERMA

Parental  PTLPKSDLNEVKELLKTNKKLAKMIGHIFEMSDDDPHKEEEIRKYSAIYGRFDSKRKDGKHLTLHELTVN
          PTLPKSDLNEVKELLKTNKKLAKMIGHIFEMSDDDPHKEEEI.K.SAIYGRFDSKRKDGKHLTLHELTVN
Retrocopy PTLPKSDLNEVKELLKTNKKLAKMIGHIFEMSDDDPHKEEEILKHSAIYGRFDSKRKDGKHLTLHELTVN

Parental  EAAAQLCVKDNALLTRRDELFALARQISREVTYKYTYRTTKSKCGERDELSPKRIK
          EAAAQLCVKDNALLTRRDELFALARQIS.EVTYKYTYRTTK.KCGERDELSPKRI.
Retrocopy EAAAQLCVKDNALLTRRDELFALARQISGEVTYKYTYRTTK*KCGERDELSPKRIR

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_2490 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010241	1 retrocopy	retro_chof_2490 ,
Callithrix jacchus	ENSCJAG00000005748	1 retrocopy	retro_cjac_4224,
Gorilla gorilla	ENSGGOG00000013842	1 retrocopy	retro_ggor_3068,
Microcebus murinus	ENSMICG00000007306	2 retrocopies	retro_mmur_1155, retro_mmur_1211,
Nomascus leucogenys	ENSNLEG00000006665	1 retrocopy	retro_nleu_2288,
Pongo abelii	ENSPPYG00000013025	1 retrocopy	retro_pabe_3822,
Ictidomys tridecemlineatus	ENSSTOG00000000098	1 retrocopy	retro_itri_1621,
Tupaia belangeri	ENSTBEG00000011954	1 retrocopy	retro_tbel_3626,