RetrogeneDB ID: retro_chof_2515

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_81480:5321..5911(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN7C
• Ensembl ID: ENSCHOG00000000111
• Aliases: None
• Description: lin-7 homolog C (C. elegans) [Source:HGNC Symbol;Acc:17789]

Sequence

>retro_chof_2515
ATGGCAGTGCTGGGGGAACCTGAGCGGCTGGAGAGAGGTATTTGTTGAGCAATTTAATTGTTGGAAAAACTACAAAGGAC
TGGAGAAGTACCACCACAAAAACTTCAGGCTTTATTATAAAGAGTCCCTCAAAGTGAGTTCTACAAGCCTGTAAGAGAGG
TTTATGAACATGTCTACGAAACAGTGGATATCAGTAGCAGTCCTGAAGTGAGAACTAATGCAACTGCAAAGGCTACAGAC
GCTGTATTTGCTGCCAATGAAGGACATTCTCATCCTTGAGTGGTTGAGCTACCAAAAACAGAAGAGGGCCTTGGATTCAA
TATCATGGGAGGGAAAGAACAAAACTCTCTAATCTATATATCTCGAATAATTCCAGGTAGTATTGCTGATAGTCATGGGT
GCCTCAAACAAAGAGACCAACTCCTTTCCGCTAATGGAGTGAGCACTGAAGGAGAATATCATGAAAAAGCTGGAGAGCTG
CTAAAAGCAGCTCAAGGAAAGGTTAAATTAATAGTATGATATACACCCAAAGTCTTAGAAGAAATGGAGTCACGATTTGA
AAAAATGAGATCAGCTAACGCAGGCAACAG

Alignment

ORF - retro_chof_2515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.34 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALGEPVRLERDICRAIELLEKLQRSGEVPPQKLQALQ-RVLQSEFCNAVREVYEHVYETVDISSSPEV
          MA.LGEP.RLER.IC.AI.LLEKLQR.GEVPPQKLQAL..RV.QSEF...VREVYEHVYETVDISSSPEV
Retrocopy MAVLGEPERLERGIC*AI*LLEKLQRTGEVPPQKLQALL*RVPQSEFYKPVREVYEHVYETVDISSSPEV

Parental  RANATAKATVAAFAASEGHSHPRVVELPKTEEGLGFNIMGGKEQNSPIYISRIIPGGIADRHGGLKRGDQ
          R.NATAKAT.A.FAA.EGHSHP.VVELPKTEEGLGFNIMGGKEQNS.IYISRIIPG.IAD.HG.LK..DQ
Retrocopy RTNATAKATDAVFAANEGHSHP*VVELPKTEEGLGFNIMGGKEQNSLIYISRIIPGSIADSHGCLKQRDQ

Parental  LLSVNGVSVEGEHHEKAVELLKAAQGKVKLVVRYTPKVLEEMESRFEKMRSAK-RRQQ
          LLS.NGVS.EGE.HEKA.ELLKAAQGKVKL.V.YTPKVLEEMESRFEKMRSA..RRQQ
Retrocopy LLSANGVSTEGEYHEKAGELLKAAQGKVKLIV*YTPKVLEEMESRFEKMRSAN<RRQQ

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_2515 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 2 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000111	7 retrocopies	retro_chof_1046, retro_chof_1062, retro_chof_1417, retro_chof_2399, retro_chof_2401, retro_chof_2515 , retro_chof_864,
Microcebus murinus	ENSMICG00000005165	2 retrocopies	retro_mmur_1590, retro_mmur_577,