RetrogeneDB ID: retro_chof_1646

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_35003:4180..4747(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC31A1
• Ensembl ID: ENSCHOG00000011908
• Aliases: None
• Description: solute carrier family 31 (copper transporter), member 1 [Source:HGNC Symbol;Acc:11016]

Sequence

>retro_chof_1646
ATGGATCATCCCACCACACAGGGATGAGCTCTATGGACCACAACGGTACCATGTCACACTCTCACCATCACCTGACCTCT
TCAGCCTCACACTTCCACAGCGGAGGAAATGGCAACATGATGATGATGATTCTTATGACTTTCTACTTTGGCTTTGAGAA
AGTGGAAATACTGTTTCAGTCTGGTGATCAATACAGCTGGAGAAATGGCTGGAGCTTTTGTGGCAGTGTTTTTACTAGCA
ATGTTCTATGAAAGACTCAAGATAGCCCGAGAGAGGTTGTTGCATAAGTCACAAGTCAGCATCTGTTTCAATTCCATGCC
TGTCCCAGGGCCTAACAGAACAATCCTTATGGAGACACCCAAAACTGCTGGGCAGCAGATGCTAAGCTTTCCTCACCTCC
TGCAAACAGTGCTGCATATTATCCAGGTGGTCATCAGCTACTTCCTCATGCTCATCTTCATGACCTACAATGGATACCTC
TGCATTGCTGTAGCAGCAGGAGTCGGTATGGGCTACTTTCTCTTCAGCTGGAAAAAGGCAGTGGTAGTGGACATCACTGA
GCACTGC

Alignment

ORF - retro_chof_1646 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.42 %
• Parental protein coverage: 99.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDH-SHHTGMSSMDLNSTTSPSHHHPTSSASHSHGGGNGNMMMMP-MTFYFGFEKVEIL-FSGLVINTAG
          MDH.SHHTGMSSMD.N.T.S.SHHH.TSSASH.H.GGNGNMMMM..MTFYFGFEKVEIL.FS.LVINTAG
Retrocopy MDH<SHHTGMSSMDHNGTMSHSHHHLTSSASHFHSGGNGNMMMMILMTFYFGFEKVEIL>FS-LVINTAG

Parental  ETAGAFVAVFLLAMFYEGLKIA-ERLLHKSQVSIHYNSMPVPGPNRTILMETHKTVGQQKLSFPHLLQTV
          E.AGAFVAVFLLAMFYE.LKIA.ERLLHKSQVSI..NSMPVPGPNRTILMET.KT.GQQ.LSFPHLLQTV
Retrocopy EMAGAFVAVFLLAMFYERLKIARERLLHKSQVSICFNSMPVPGPNRTILMETPKTAGQQMLSFPHLLQTV

Parental  PHVIQVVISYFLMLIFMTCNGYLCIAVAAGASTGYFLFSWKTTVVVDITEHC
          .H.IQVVISYFLMLIFMT.NGYLCIAVAAG...GYFLFSWK..VVVDITEHC
Retrocopy LHIIQVVISYFLMLIFMTYNGYLCIAVAAGVGMGYFLFSWKKAVVVDITEHC

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_1646 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 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011908	5 retrocopies	retro_chof_1186, retro_chof_1646 , retro_chof_1661, retro_chof_644, retro_chof_776,
Felis catus	ENSFCAG00000005512	1 retrocopy	retro_fcat_425,
Macropus eugenii	ENSMEUG00000015425	2 retrocopies	retro_meug_1049, retro_meug_1533,
Microcebus murinus	ENSMICG00000015008	2 retrocopies	retro_mmur_1465, retro_mmur_46,
Myotis lucifugus	ENSMLUG00000015299	1 retrocopy	retro_mluc_2,
Nomascus leucogenys	ENSNLEG00000016636	1 retrocopy	retro_nleu_622,
Pongo abelii	ENSPPYG00000019514	3 retrocopies	retro_pabe_2386, retro_pabe_3548, retro_pabe_847,
Sorex araneus	ENSSARG00000012787	7 retrocopies	retro_sara_101, retro_sara_326, retro_sara_497, retro_sara_584, retro_sara_585, retro_sara_586, retro_sara_730,
Tupaia belangeri	ENSTBEG00000009011	2 retrocopies	retro_tbel_3123, retro_tbel_4170,