RetrogeneDB ID: retro_chof_2278

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_6295:9576..10360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000009884
• Aliases: None
• Description: None

Sequence

>retro_chof_2278
ATGAAGCTCATCGTCCTTGACAACTATTCTTGGGCCAGTGAGTGGGCAGTCAAATATATCAGGAACCATGTCATCCAGTT
TAACCCAGGGCCAGACAAGTACTTCACCCTGGGGCTCCCCACTGGGAACACCCCTCTTGGCTTCTACAAGAAGCTGACTG
AGTACCACGAGAACAATCACCTGGCCTTCAAACATGTGAAGACCTTCAACATGGACAAGTATGTGGGTCTTCCTTGAGAC
CACTCAGAGAGTTACCACTCCATGTGGAACAACTTCTTCAAGCACACTGACAGCCATCCAGAAAACCTGAATATTCTGGA
CAGGAATGCAGCTGACCTGCAGGTTGAGGGTTGTACCACCAAAGAAGAGATCACAGCTGTGGGCGGGATCGAGCTGTTTG
TTGGAGGCATTGGCCCCAAAGGACACATCACCTTCAATGATCTGGGCTCCAGTCTGGCATCCAGAATCCATGTGAAGATG
TTGGCCACGGGCAGCATCTTGGCTAACGCTGGGTTCTTCGATGGAGATCTCACCAAGGAGCCTGCCATGGCCCTGATGGT
GGGCGTGGGCACCATCACGGATGCTAGAGAGGTGACGAACCTCATGTTGACAGGCACAAGGCGTTTGCTCTGTACAAAGT
CATTGAGAAAGGGTGAACCATATGGGGATCATGTCTGCTCTTCTGCAGCATCCCCACACAGTGTTTGTGTGTGTTGAGGA
TGCTACCCTAGAGCTGAAAGTGAAATCCGTCAAGTACTTCCAAGATTTAATGCTTGTTCATAAC

Alignment

ORF - retro_chof_2278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.96 %
• Parental protein coverage: 91. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKLIILDDYSQASEWAAKYIRNRIIQFNPGPDKYFTLGLPTGSTPLGCYKKLIEYYRNGDLSFKYVKTFN
          MKLI.LD.YS.ASEWA.KYIRN..IQFNPGPDKYFTLGLPTG.TPLG.YKKL.EY..N..L.FK.VKTFN
Retrocopy MKLIVLDNYSWASEWAVKYIRNHVIQFNPGPDKYFTLGLPTGNTPLGFYKKLTEYHENNHLAFKHVKTFN

Parental  MDEYVGLPRDHPESYHSFMWNNFFKHIDIHPENTHILDGNAADLKVECDAFEEKITAAGGIELFVGGIGP
          MD.YVGLP.DH.ESYHS.MWNNFFKH.D.HPEN..ILD.NAADL.VE.....E.ITA.GGIELFVGGIGP
Retrocopy MDKYVGLP*DHSESYHS-MWNNFFKHTDSHPENLNILDRNAADLQVEGCTTKEEITAVGGIELFVGGIGP

Parental  DGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFDGDLTKVPTMALTVGVGTIMDAREVMILI-TGAHKA
          .GHI.FN..GSSL.SR..VK.LA...ILANA.FFDGDLTK.P.MAL.VGVGTI.DAREV..L.....HKA
Retrocopy KGHITFNDLGSSLASRIHVKMLATGSILANAGFFDGDLTKEPAMALMVGVGTITDAREVTNLM<VDRHKA

Parental  FALYKAIEEG-VSHMWTVSAFQQHPRTVFVCDEDATLELKVKTVKYFKGLMLVHN
          FALYK.IE.G.V.HM...SA..QHP.TVFVC.EDATLELKVK.VKYF..LMLVHN
Retrocopy FALYKVIEKG<VNHMGIMSALLQHPHTVFVCVEDATLELKVKSVKYFQDLMLVHN

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_2278 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007865	1 retrocopy	retro_btau_535,
Choloepus hoffmanni	ENSCHOG00000009884	2 retrocopies	retro_chof_2278 , retro_chof_42,
Dasypus novemcinctus	ENSDNOG00000007804	3 retrocopies	retro_dnov_1363, retro_dnov_1608, retro_dnov_508,
Macropus eugenii	ENSMEUG00000015442	1 retrocopy	retro_meug_655,
Monodelphis domestica	ENSMODG00000010398	1 retrocopy	retro_mdom_1337,
Mus musculus	ENSMUSG00000052102	1 retrocopy	retro_mmus_2711,
Oryctolagus cuniculus	ENSOCUG00000016963	1 retrocopy	retro_ocun_1266,
Otolemur garnettii	ENSOGAG00000007303	3 retrocopies	retro_ogar_2251, retro_ogar_2506, retro_ogar_446,
Ictidomys tridecemlineatus	ENSSTOG00000016508	1 retrocopy	retro_itri_1135,
Tupaia belangeri	ENSTBEG00000003330	2 retrocopies	retro_tbel_2431, retro_tbel_59,