RetrogeneDB ID: retro_chof_1310

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_25906:3624..4654(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSCHOG00000001608
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]

Sequence

>retro_chof_1310
AAGCCAGTCAGCTGGGCTGATGAAACAGATGACCTAGAAGGAGATGTTTCAACCACTTGGCACAGTAATGATGATGATGT
GTATAGGGTACCTCCAATTGACCATTCCATCCTCCCCACTGCTCCACGGGCTGCTCGGGAACCCAATATCCACTGGAGCT
GTCTTCTCAAATCACCATCCTACACTGCCCTTCTAGGGAACCTGCCCTATGATGTGACAGAAGACTCCATTTAGGAATTC
TTTAGAGGATTAAATATCAGTGCAGTGCATTTATCATGTGTACACAGCAATCCAGGGAGGTTGAAATGTTTTGGTTATGC
CAAGTTTGTGGACCTGGATTCCCTATTCAGTGCCCTGAGCCTCAATGAAGAGTCTCTAGGCAACAGGAGAATTTGAGTGG
ACGTTGCTGATCAAGCACAGGATAAGGACAGGGATGATCATTCTTTTGGCCAAGATAGAAATTGGGACTCTGACAAAACA
GATACAGACTGGAGGGCCCATCCTGCCACAGACAGCTTTGCTGACTACCCACCTAGAAAAAGTGACGATAGCTTTGGAGA
CAAGTATCGTGATCGTTATGATTCAGACCGGGTATTGTGATTGATATCGTGACGGTTATTGTGACGGCCCACACGGGGAT
GTCGGTCGATATGGAGGCTGGGATCACTATGATGACTGAGGCAGAAGAGACTATGATAGAGGCTATGACTCCAGGATAGG
CAGAAGCAGAAGAGCATTTGGGAGTGAGTACCACAGGGATGATGACCGGAGGAGGTGGGGACCGCTATGAAGACCAATAG
GACAGATGGATGATCAGTCATGGAGCGACATAGATGATTACTCCCCAGATGATTATAGGCTTGAAGATAGAGGTCCCCAC
CTCCCCCCAAGATCCAAACTGAATCTAAAGCCTCGGAATACTCCTAAGGAAGTTGTTTCCTCTGCTAGCATTTCCCAATC
CAGTAGAGCAGCTTCTGTCTTTGGAGAGGCAAAGCCTACTGACATGGCAGCTAGAGAACAGGAGGTAGAG

Alignment

ORF - retro_chof_1310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.4 %
• Parental protein coverage: 55.97 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRSILPTAPRAAREPNIDRSRLPKSPPYTAFLGNLPY
          KPVSWADETDDLEGDVSTTWHSNDDDVYR.PPID.SILPTAPRAAREPNI..S.L.KSP.YTA.LGNLPY
Retrocopy KPVSWADETDDLEGDVSTTWHSNDDDVYRVPPIDHSILPTAPRAAREPNIHWSCLLKSPSYTALLGNLPY

Parental  DVTEDSIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLFSALSLNEESLGNRRIRVDVADQAQ
          DVTEDSI.EFFRGLNISAV.L....SNP.RLK.FGYA.F.DLDSLFSALSLNEESLGNRRI.VDVADQAQ
Retrocopy DVTEDSI*EFFRGLNISAVHLSCVHSNPGRLKCFGYAKFVDLDSLFSALSLNEESLGNRRI*VDVADQAQ

Parental  DKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDDYPPRRGDDSFGDKYRDRYDSDR-YRDGYRDGYRDG
          DKDRDD.SFG.DRN.DSDKTDTDWRA.PATDSF.DYPPR..DDSFGDKYRDRYDSDR.Y.D.YRDGY.DG
Retrocopy DKDRDDHSFGQDRNWDSDKTDTDWRAHPATDSFADYPPRKSDDSFGDKYRDRYDSDR>YCD*YRDGYCDG

Parental  PRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGSGYRRDDDYR-GGGDRYEDRYDR-RDDRSWSS
          P..D..RYGG.D.YDD.G.RDYDRGYDSRIG..RRAFGS.Y.RDDD.R.GG.DRYED..DR..DD.SWS.
Retrocopy PHGDVGRYGGWDHYDD*GRRDYDRGYDSRIGRSRRAFGSEYHRDDDRR>GG-DRYEDQ*DR<MDDQSWSD

Parental  RDDYSRDDYRRDDRGP--PQRPKLNLKPRSTPKEDDSSASTSQSSRAASIFGGAKPVDTAAREREVE
          .DDYS.DDYR..DRGP..P.R.KLNLKPR.TPKE..SSAS.SQSSRAAS.FG.AKP.D.AARE.EVE
Retrocopy IDDYSPDDYRLEDRGPHLPPRSKLNLKPRNTPKEVVSSASISQSSRAASVFGEAKPTDMAAREQEVE

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_1310 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012023	2 retrocopies	retro_amel_1107, retro_amel_559,
Canis familiaris	ENSCAFG00000007117	2 retrocopies	retro_cfam_1447, retro_cfam_936,
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310 , retro_chof_366,
Choloepus hoffmanni	ENSCHOG00000002525	2 retrocopies	retro_chof_1279, retro_chof_1903,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,