RetrogeneDB ID: retro_chof_1088

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_196842:11..526(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPQ
• Ensembl ID: ENSCHOG00000000345
• Aliases: None
• Description: centromere protein Q [Source:HGNC Symbol;Acc:21347]

Sequence

>retro_chof_1088
GCAAAAAATGTTAAAGATTTGGAACAAATCCAGTATCATCTCCACTGCTTGAACAAAAGATTCTACAGCAGTGTGAAATG
CTAGAATTCCCTCCCAAAAAGCAGAAAGATTTAACTAATGTGTCAAGTCTACAGAAAATGGAAAGGACACAGCACAGAGC
TAATGAAGAAGGTCTGGCATTATCGCAGGAAGAAATAGATAAAATAGTGGAGACCGCAGAGTCAATGACTGGGAATATTC
AAAGCCTCAAAAGCAAACTTCAGATTCTGACAAGTGAGGTGGAAGAAGAGGAGGAGAAGGTAAAACAGATATTTCAAATG
CATAGTAGTGAGGTACTCTCTCTTCCAGAACTTTTTCAGAACAGTCTCAAAGCACCAATACTTCAGAAAGAAATTTTGAT
GCTAATCCCAAACCAGAATGCTCTTCTAAAGGACTTGGATGTTATTCATTATTCATCCCAGATGAAGGATATGTTCCCTT
TCATTGAAGAAGACTACAAGGGACTTGATGCCTCC

Alignment

ORF - retro_chof_1088 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.97 %
• Parental protein coverage: 64.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKSIKENEQIQYHLNCLNKR-LLQLCETLDVPPKKQKDLTNVSSLLKMERTQHRANEEGLALLQEEIDKI
          .K..K..EQIQYHL.CLNKR..LQ.CE.L..PPKKQKDLTNVSSL.KMERTQHRANEEGLAL.QEEIDKI
Retrocopy AKNVKDLEQIQYHLHCLNKR<ILQQCEMLEFPPKKQKDLTNVSSLQKMERTQHRANEEGLALSQEEIDKI

Parental  VETTESMTGNIQSLKSKLQVLTSEVDEEEEKVKNIFQMDGSEVLSLPELSQNSLKAPILQKEILMLIPNQ
          VET.ESMTGNIQSLKSKLQ.LTSEV.EEEEKVK.IFQM..SEVLSLPEL.QNSLKAPILQKEILMLIPNQ
Retrocopy VETAESMTGNIQSLKSKLQILTSEVEEEEEKVKQIFQMHSSEVLSLPELFQNSLKAPILQKEILMLIPNQ

Parental  NALLKDLDVLHNSSQMKDMFTFIEEAYKRLDAS
          NALLKDLDV.H.SSQMKDMF.FIEE.YK.LDAS
Retrocopy NALLKDLDVIHYSSQMKDMFPFIEEDYKGLDAS

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_1088 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000345	1 retrocopy	retro_chof_1088 ,
Oryctolagus cuniculus	ENSOCUG00000006103	1 retrocopy	retro_ocun_32,
Ictidomys tridecemlineatus	ENSSTOG00000001426	1 retrocopy	retro_itri_1111,
Tupaia belangeri	ENSTBEG00000004322	1 retrocopy	retro_tbel_1115,