RetrogeneDB ID: retro_chof_557

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_121296:983..1937(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGM2L1
• Ensembl ID: ENSCHOG00000009209
• Aliases: None
• Description: phosphoglucomutase 2-like 1 [Source:HGNC Symbol;Acc:20898]

Sequence

>retro_chof_557
TGGGATGATTCTTTAGTTGATGGCAGTTCACTTATTCTTGACCCAAGTGCTTCCATTTATAAGGCCTGCTTTGAAGACCT
TAAGAAATATTGTTTTCATTGCAGTGTGAGCAGGGAGACCACGGTGACGTTTGTGCACACTTCTGTGCACGGCGGGTGTC
ATGACCTTGTGCCATGAGCTTTCAAAGCTGTGGTCTTTGCTCCTCCCTTGGGCAGTTCCAAACAGAAAGATTCTGATTCC
AAGTTTCCAACCGTGAATTACCTGAATTCTGATGTGTGTAAAGGGGTGTTGACTTTATCTTTTGGTTTGGCAGACAAAAC
CAAAGCCAAAATTGTTTTGGCAAATAACCCAGATGCTGATAGTCCAGCTGTAGAAGAATAGCCAGACAGCAGTGAATGCA
GAGTGTTTTCTGGCAATGAACTGGGAGCCCTTTGGGGCTGGTGGCTCTTTATCTCTTGAGAAAAAAAGAACCAAAATCCA
AGTGCCCTCAAGACATGTAAACGTCATCCAGCACCATCTCCTCCAAAATCTTGTGGGCCATTGCTTTAATGGAAGGTTTT
CATTTTGAGGGAGCATTAACTGACTTTAATGGATGGGAAACAGAGCCAAACTACTAAACCAAGATAAAAATGTTTAATTT
GCATTTGAAGAGGCTATTGGATACACGTGCTGCCCTGTTGTTCTGGACAAAGATGGAGTCAGTGCTGCAGAGTTGACTAG
CTTTTTAGCAACCAAGAATTTGTCTTTGTCGCAGCAGCTAAAGGCCATCTATGCTGAGTACATCTACCATATTACCAAAG
CCTCATATTTTATCTGCCATGATCAAGGCATCATTAAAAATTATTTGAATACCTTAGAAATTACAATAAGAATAACTATC
CCAAAATTTGTGGTATATATGAAATTTCTGGCATCAGGGACCTTACAACTGGCTATGATGATAGCCAACCCAAC

Alignment

ORF - retro_chof_557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.61 %
• Parental protein coverage: 52.17 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WNDNLVDTSPLKKDPLQDICKRYMEDLKKICFHRVLNSKTTLKFVHTSFGVG-HDYVQLAFQVFGFKPPI
          W.D.LVD.S.L..DP...I.K...EDLKK.CFH......TT..FVHTS...G.HD.V..AF....F.PP.
Retrocopy WDDSLVDGSSLILDPSASIYKACFEDLKKYCFHCSVSRETTVTFVHTSVHGGCHDLVP*AFKAVVFAPPL

Parental  PVPEQKDPDPDFSTVKCPNPEEGESVLELSLRLAEKENARIVLATDPDADRLAVAELQENGHWKVFTGNE
          ....QKD.D..F.TV...N......VL.LS..LA.K..A.IVLA..PDAD..AV.E........VF.GNE
Retrocopy GSSKQKDSDSKFPTVNYLNSDVCKGVLTLSFGLADKTKAKIVLANNPDADSPAVEE*PDSSECRVFSGNE

Parental  LAALFGWWMFDCWKKKESRNADMK-DVYMLATTVSSKILKAIALKEGFHFEETLPGFK-WIGSRIKYLLE
          L.AL.GWW.F....KK.......K.D......T.SSKIL.AIAL.EGFHFE..L..F..W.G.R.K.LL.
Retrocopy LGALWGWWLFIS*EKKNQNPSALK<DM*TSSSTISSKILWAIALMEGFHFEGALTDFN<WMGNRAK-LLN

Parental  SGKEVLFAFEESIGFLCGTSVLDKDGVSAAVVVAEMASYLETMNITLKQQLIKVYEKYGYHITKTSYFLC
          ..K.V.FAFEE.IG..C...VLDKDGVSAA....E..S.L.T.N..L.QQL...Y..Y.YHITK.SYF.C
Retrocopy QDKNV*FAFEEAIGYTCCPVVLDKDGVSAA----ELTSFLATKNLSLSQQLKAIYAEYIYHITKASYFIC

Parental  YDPPTIKS-IFERLRNFDAPKEYPKFCGMFAVLHVRDVTTGYDSSQPN
          .D...IK...FE.LRN......YPK.CG.......RD.TTGYD.SQPN
Retrocopy HDQGIIKN<LFEYLRNYN-KNNYPKICGIYEISGIRDLTTGYDDSQPN

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_557 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 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009209	1 retrocopy	retro_chof_557 ,
Choloepus hoffmanni	ENSCHOG00000011458	1 retrocopy	retro_chof_612,
Tarsius syrichta	ENSTSYG00000002928	7 retrocopies	retro_tsyr_1740, retro_tsyr_1839, retro_tsyr_2095, retro_tsyr_2112, retro_tsyr_2119, retro_tsyr_721, retro_tsyr_849,