RetrogeneDB ID: retro_chof_1882

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_413516:2..902(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPDL1
• Ensembl ID: ENSCHOG00000013141
• Aliases: None
• Description: spindle apparatus coiled-coil protein 1 [Source:HGNC Symbol;Acc:26010]

Sequence

>retro_chof_1882
TTGCTACAGATGAAAGGGTCTCAGTCTGAATTTGAACAGCAGGAATGGTTGCTTGCCATGTTGGAGCAGAAAAATGGTGA
AATGAAACATCTTTAGGTGAAATAAGTTTGGAGAAATTTAAGAGTTTATATGAAAGTATGGAATCTAAATCTTCATCCAA
CTCGGGCATTCTGGAAGATAACACCTATTATACAGATTTACTTCAGATAAAACTTGATAACTTAAACAAAGAAAATGAAA
GCACTAAAGGCGAACTCTCTATACAGCGAATGAAAGCATTATTTGAGAGCCAGCGGGCTCTGGATATTGAGCGAAAGCTT
TTTGCAAATGAAAGATGCCTCCAGCTCTCCCAAAGTGAAAATATGAAACTGAGAGCTAAACTAGATGAATTAAAGCTGAA
GTATGAACCTGAAGAGAAAATTGAAGTGCCTGTACTCAAAAAGAGGCGTGAGGTACTGCCTGTGGATGTAACCACTTCTA
AAGATGTATGTGACAACTGTGCTGTCAGGGAAGAAATGTATAGATTGCCGACTCTGAAAGAGGAGGCACAATCATGTTCT
AACAATTTAGAAGACAACAACCTGCAGTTAGAAAAGACAGTTTCTGTAAACACACCAGTAGTCAGTCTCTCACCTAACAA
AAATCTATCAACGAATATGCAACCAGCGAAGGAAAAGAAATGTGTGAAACTCACAGGAGTTCCAGCTGACTCTGAAGTCT
TAAGTGAAAGAAGTGGAAACACCCCTAACTCTTCCAGGTTAGCTGCTGAATCAAGGCTTCAAACAGAAGTTCAAGAAGGG
AAGGAAACTGCAAGCAAATTGGAAAAGGAAACTTGTAAGAATCACACCCTATTCTATACGTATCCTCCAATCGACTCCAG
AGACACAGTGCCCTCAGCAG

Alignment

ORF - retro_chof_1882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.41 %
• Parental protein coverage: 50.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LLQMKGSQSEFEQQERLLAMLEQKNGEIKHL-LGEIRSLEKFKSLYESMESKSSSNSGILEDNTYYTDLL
          LLQMKGSQSEFEQQE.LLAMLEQKNGE.KHL.LGEI.SLEKFKSLYESMESKSSSNSGILEDNTYYTDLL
Retrocopy LLQMKGSQSEFEQQEWLLAMLEQKNGEMKHL<LGEI-SLEKFKSLYESMESKSSSNSGILEDNTYYTDLL

Parental  QIKLDNLNKENESTKGELSIQRMKALFESQRALDIERKLFANERCLQLSQSENMKLRAKLDELKLKYEPE
          QIKLDNLNKENESTKGELSIQRMKALFESQRALDIERKLFANERCLQLSQSENMKLRAKLDELKLKYEPE
Retrocopy QIKLDNLNKENESTKGELSIQRMKALFESQRALDIERKLFANERCLQLSQSENMKLRAKLDELKLKYEPE

Parental  EKIEVPVLKKRREVLPVDITTSKDVCDNCAVREEVYRWPTLKEEAQTCSNNLEDNNLQLEKTVSINTPVV
          EKIEVPVLKKRREVLPVD.TTSKDVCDNCAVREE.YR.PTLKEEAQ.CSNNLEDNNLQLEKTVS.NTPVV
Retrocopy EKIEVPVLKKRREVLPVDVTTSKDVCDNCAVREEMYRLPTLKEEAQSCSNNLEDNNLQLEKTVSVNTPVV

Parental  SLSPNKNLSTNMQPTKEKKCVKLTGVPADSEVLSERSGNTPNSSRLAAESRLQTEVQEGKETASKLEKET
          SLSPNKNLSTNMQP.KEKKCVKLTGVPADSEVLSERSGNTPNSSRLAAESRLQTEVQEGKETASKLEKET
Retrocopy SLSPNKNLSTNMQPAKEKKCVKLTGVPADSEVLSERSGNTPNSSRLAAESRLQTEVQEGKETASKLEKET

Parental  CK-KSHPILYVSS-KSTPETQCPQQ
          CK..SHPILYVSS..STPETQCPQQ
Retrocopy CK<ESHPILYVSS<QSTPETQCPQQ

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_1882 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013141	5 retrocopies	retro_chof_1356, retro_chof_1565, retro_chof_1882 , retro_chof_198, retro_chof_2505,
Callithrix jacchus	ENSCJAG00000004745	1 retrocopy	retro_cjac_766,