RetrogeneDB ID: retro_chof_612

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_126730:6097..6761(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGM2
• Ensembl ID: ENSCHOG00000011458
• Aliases: None
• Description: phosphoglucomutase 2 [Source:HGNC Symbol;Acc:8906]

Sequence

>retro_chof_612
ACTTTATCTTTTGGTTTGGCAGACAAAACCAAAGCCAAAATTGTTTTGGCAAATAACCCAGATGCTGATAGTCCAGCTGT
AGAAGAATAGCCAGACAGCAGTGAATGCAGAGTGTTTTCTGGCAATGAACTGGGAGCCCTTTGGGGCTGGTGGCTCTTTA
TCTCTTGAGAAAAAAAGAACCAAAATCCAAGTGCCCTCAAAGACATGTAAACGTCATCCAGCACCATCTCCTCCAAAATC
TTGTGGGCCATTGCTTTAATGGAAGGTTTTCATTTTGAGGGAGCATTAACTGACTTTAATGGATGGGAAACAGAGCCAAA
CTACTAAACCAAGATAAAAATGTTTAATTTGCATTTGAAGAGGCTATTGGATACACGTGCTGCCCTGTTGTTCTGGACAA
AGATGGAGTCAGTGCTGCAGAGTTGACTAGCTTTTTAGCAACCAAGAATTTGTCTTTGTCGCAGCAGCTAAAGGCCATCT
ATGCTGAGTACATCTACCATATTACCAAAGCCTCATATTTTATCTGCCATGATCAAGGCATCATTAAAAATTATTTGAAT
ACCTTAGAAATTACAATAAGAATAACTATCCCAAAATTTGTGGTATATATGAAATTTCTGGCATCAGGGACCTTACAACT
GGCTATGATGATAGCCAACCCAAC

Alignment

ORF - retro_chof_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 50.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TLSF-LADKTKAKIVLANAPDADRLAVAEKQDSGEWKVFSGNELGALLG-WWLFTSWKNFPYFSALKD--
          TLSF.LADKTKAKIVLAN.PDAD..AV.E..DS.E..VFSGNELGAL.G.W......K.....SALKD..
Retrocopy TLSFGLADKTKAKIVLANNPDADSPAVEE*PDSSECRVFSGNELGALWGWWLFIS*EKKNQNPSALKDM*

Parental  TYMSPVSSKILRAIALKXXXXXXETLTGFK-WMGNRAKQLIDQGKNVLFAFEEAIGYMCCPFVLDKDGVS
          T..S..SSKIL.AIAL.........LT.F..WMGNRAK.L..Q.KNV.FAFEEAIGY.CCP.VLDKDGVS
Retrocopy TSSSTISSKILWAIALMEGFHFEGALTDFN<WMGNRAK-LLNQDKNV*FAFEEAIGYTCCPVVLDKDGVS

Parental  AAVICAELASFLATKNLSLSQQLNAIYVEYGYHITKASYFICHDQGMIK-KLFENLRNYDGKNNYPRTCG
          A....AEL.SFLATKNLSLSQQL.AIY.EY.YHITKASYFICHDQG.IK.KLFE.LRNY..KNNYP..CG
Retrocopy A----AELTSFLATKNLSLSQQLKAIYAEYIYHITKASYFICHDQGIIK<KLFEYLRNYN-KNNYPKICG

Parental  KYEISGIRDLTAGYDDSQPD
          .YEISGIRDLT.GYDDSQP.
Retrocopy IYEISGIRDLTTGYDDSQPN

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_612 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	ENSCHOG00000009209	1 retrocopy	retro_chof_557,
Choloepus hoffmanni	ENSCHOG00000011458	1 retrocopy	retro_chof_612 ,
Microcebus murinus	ENSMICG00000012334	1 retrocopy	retro_mmur_1240,
Monodelphis domestica	ENSMODG00000020527	1 retrocopy	retro_mdom_110,