RetrogeneDB ID: retro_chof_697

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_136553:4158..4901(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFCP2L1
• Ensembl ID: ENSCHOG00000000115
• Aliases: None
• Description: transcription factor CP2-like 1 [Source:HGNC Symbol;Acc:17925]

Sequence

>retro_chof_697
CTCTTCCAGCACAGGCAGCCTGAGCTTGACAATCAGCACAACTCCAGCACCTATCTGCGCCATGTCCTCGCTCTGCCCAT
CTTCAAGCGGGAGGAGCCCCAGCTGTCCCCTGAGAACGAGGCCCACCTGCAGCCCTTGCAGTATGTGCTGTGTGCCCCGA
CGTCCCCTGGACGAAGAGATGCTGACCTACCTCAACCAAGGTCAGTCTTATGAAATCCAACTCCTGGAGAATCGAAGGTG
GGAGATTTTCTAGATCTGAACACAAAATATGTCAAGAACATCATCTGCATGGTTTTCCATGACCATCGGCTGCAGTATAT
GGAGCACCAGCAGCTGGAGGGCTGGAGGTGGAGCCGGCCTGGAGACCGGATCCTGGACCTTGGTATTCTACTGTCTGTTG
GTATCTTGGACCCCAGGACCAGCCGAACCCAGTTGAACACTGTCAAGTTTTTGTGGGACCCTTCGAAGAGAGCCTCTGCC
TTCCTTCAGATGCACGGCACATCAGCAAGGAATTCACCCTGAGGAAGCACGCGGGCTAGAAGGGGGTGACTTTCCGCGTG
CAGATCGATAAGCAGAAGGCGATTGATTACCTGCACTCTGCCAGCTGCCTGGTGAAGGTGTTCAAGCCAAAGGGAGCCAA
CCGGAAGCAGAAGACTGACTAGGAGAAGAAGGAGAAAAGAACTGCCCAAGAGAAGATGTACCAGCTGTCCTACAAGACCA
CTGTCCTCATGGAGTGCTCTCCA

Alignment

ORF - retro_chof_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.51 %
• Parental protein coverage: 57.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LFRQRQSEQNIQHKSGSYLPDVLALPIFKQEEPQLSPE-EARLPPLQYVLCATF-PELQEETPDLNK-QS
          LF..RQ.E...QH.S..YL..VLALPIFK.EEPQLSPE.EA.L.PLQYVLCA...P...E....LN..QS
Retrocopy LFQHRQPELDNQHNSSTYLRHVLALPIFKREEPQLSPENEAHLQPLQYVLCAPT>PLDEEMLTYLNQGQS

Parental  YEIRLLENR-KLGDFQDVNTKXXXRV---VFRDCRLQSTEHQQREGWRWS-GGDRVPGTDSAPSVGMLDH
          YEI.LLENR.K.GDF.D.NTK........VF.D.RLQ..EHQQ.EGWRWS..GDR........SVG.LD.
Retrocopy YEIQLLENR<KVGDFLDLNTKYVKNIICMVFHDHRLQYMEHQQLEGWRWSRPGDRILDLGILLSVGILDP

Parental  SASPIQLNTIGFRWGPSKRASAFSKVHCISTEFTP-RKQGGKRG-VPFRVQIDRFKSKSREYMDHLYSSC
          ..S..QLNT..F.W.PSKRASAF...H..S....P.......RG.V.FRVQID..K.K...Y......SC
Retrocopy RTSRTQLNTVKFLWDPSKRASAFLQMHGTSARNSP*GSTRARRG<VTFRVQID--KQKAIDYLHS--ASC

Parental  HIKVFQPKGGDQKQRSAGEGMEKRTAQEKKCP-SYETTILTEGPP
          ..KVF.PKG...KQ....E..EKRTAQEK....SY.TT.L.E..P
Retrocopy LVKVFKPKGANRKQKTD*EKKEKRTAQEKMYQLSYKTTVLMECSP

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_697 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000115	1 retrocopy	retro_chof_697 ,