RetrogeneDB ID: retro_chof_271

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5952:35532..36337(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S2
• Ensembl ID: ENSCHOG00000006521
• Aliases: None
• Description: eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa [Source:HGNC Symbol;Acc:3266]

Sequence

>retro_chof_271
ACAGAAGAAACCCAGCCCTCAGAAACAAAAGAAGTAGAGCCAGAGCCAACTGAGGACTAAGATGTGGAAGCTGATGAAGA
GAACAGTAGGAAAAAGGATGCATCTGATGATCTAGATGACTTGAATTTTTTAATCAAAAGAAAAAGAAGAAAAAAACAAA
AAAGATATTTGATATTGATGAAGCTGAAGAAGATATAAAGGAGTTAAAGATTGAAAGTGATATTCAAGAACCAGCTGAAC
CAGAATATGACTTTGACATTATGTTTGGCATAATGTCAGAAGAAGAAGAAAAAGAAGAATGTCAAGTTCCCAGATGAGGA
TGAAACACTAGAGAAAGATGAAACTTTAGAAGATGAAGATAGCAAAAAGGATGATGGTATCTCATTCAGTAATCAGACAG
GCCCTGCTTGGGCAGGATCAGAAAAAGACTATACATATGAGGAGTTACTGAATCGAGTTTTCAGCATCATGAGGGAAAAG
AATCCAGATATGGTTGCTGGAGAGAAAAGGAAATTTGTCATGAAACCTCCACAGGTTGTCCGAGTAGGAACCGAAAAAAC
ATCTTTTGTCAACTTTACAGATATCTGTAAACTATTACATTGTCAGCCTAAACATCTCCTTGCATTTCTATTGGCTGAAT
TGAGTACAAGTAGTTCTATAGATGGTAATAACCAACTTGTAATTAAAGGAAGATTCCAACAGAAACAGACAGAAAATGTC
TTGAGAAGATATATCAAGGAATATGTCACCTGTCACACATGCCGATCACCAGACGGCAATCCTGCAGAAGGACACCCGAC
TCTAT

Alignment

ORF - retro_chof_271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.35 %
• Parental protein coverage: 79.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TEETQPSETREVEPEPTEDKDMEADEDDSRKKDASDDLDDLNF-FNQKKKKKKTKKIFDIDEAEEGIKEL
          TEETQPSET.EVEPEPTED.D.EADE..SRKKDASDDLDDLNF.FN..........IFDIDEAEE.IKEL
Retrocopy TEETQPSETKEVEPEPTED*DVEADEENSRKKDASDDLDDLNF<FNXXXXXXXXXXIFDIDEAEEDIKEL

Parental  KIESDIQEPAEPEDDLDIMLGNK-KKKK--KNVKFPDEDEILEKDEALEDEDSKKDDGISFSNQTGPAWA
          KIESDIQEPAEPE.D.DIM.G....KKK..KNVKFPDEDE.LEKDE.LEDEDSKKDDGISFSNQTGPAWA
Retrocopy KIESDIQEPAEPEYDFDIMFGIM>QKKKKKKNVKFPDEDETLEKDETLEDEDSKKDDGISFSNQTGPAWA

Parental  GSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVVRVGTKKTSFVNFTDICKLLHRQPKHLLA
          GSE.DYTYEELLNRVF.IMREKNPDMVAGEKRKFVMKPPQVVRVGT.KTSFVNFTDICKLLH.QPKHLLA
Retrocopy GSEKDYTYEELLNRVFSIMREKNPDMVAGEKRKFVMKPPQVVRVGTEKTSFVNFTDICKLLHCQPKHLLA

Parental  FLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVTCHTCRSPD-TILQKDTRLY
          FLLAEL.TS.SIDGNNQLVIKGRFQQKQ.ENVLRRYIKEYVTCHTCRSPD..ILQKDTRLY
Retrocopy FLLAELSTSSSIDGNNQLVIKGRFQQKQTENVLRRYIKEYVTCHTCRSPD>AILQKDTRLY

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_271 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007498	1 retrocopy	retro_cfam_2070,
Choloepus hoffmanni	ENSCHOG00000006521	1 retrocopy	retro_chof_271 ,
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196, retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101,
Myotis lucifugus	ENSMLUG00000005335	1 retrocopy	retro_mluc_604,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Mus musculus	ENSMUSG00000074656	1 retrocopy	retro_mmus_3200,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,
Tupaia belangeri	ENSTBEG00000009970	2 retrocopies	retro_tbel_1505, retro_tbel_2508,