RetrogeneDB ID: retro_chof_2231

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_59842:648..1634(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSCHOG00000000867
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 2 [Source:HGNC Symbol;Acc:9650]

Sequence

>retro_chof_2231
GATCATAACTGTGTTGAGCTGCAGATTGCTGAAAATGATTTTATCAACACCAGCTTGGTCAATATTAAAGAGGTGCAGAG
GAGCTATATCCTAACCCAGGGTCTACTTCCTAATATGTGTTGTCATTTCTGGCTCATGATTTGGCAGCAAAAGACCAAAG
CAGTCATCATGCTGAACCAAGTTGTGGAGCTGAACCAAGTTGTTAAATGTGCACAGTACTAGCCAACAAAAGATGACCAA
GAGATGGTGTTTAAAGAAACACGATTCAGTGTGAAGCTCTTGTCAGAAGATGTAAAATCATATAATACAGTATATCGACT
ACAATTAGAAAACATCAATAGTGGAGAAGCAGAATAATATTTCACTTTCATCACACTACCTGGACAGATTTTGGAGTCCC
TGAATCACCAGCTTCCTTTCTCAATTTCTCATTTAAAGTGAGAGAGTCTGGCTCTTTGAACTCTGAGCACAGGCCTGCAG
TGGTCCACAGTAGTGCAGGAATTGGGCAGTCTGGCACCTTTTCATTGGTGGACACTTGTCTGGTTTTGATGGAAAAAGGA
GATGATATTAATATTAAAAAAGTTTTACCAAAAATGAAGAAATATCAAATGGGACTTATTCAGACCCCAGATCAACTCAG
AATCTCATATATGGCTATACTAGAAGGGGCAAAGTTTATAAAGGGAGATTCAAATATAGACAAACAGTAGAAAGAACATT
CTAAGTAATATTTATCTCCTGGTTTTGATCTTTCACCAACCAAAATAATGATTGAAAAATACAATGGGAACAGAATAGTC
TTAGAAGAAGAAAAACTGGCAGGTGACAGATGTAAAGGATTGTCCTCTAAAATGCAAGATACTGTGGAAGAAAACAGTGA
GAGTGTTCTATGGAAACATATTTGAGAGGACAGAAGAGCTAACACAGCTCAGTAGATGCAGCAGATGAAGCAGAGGCCAA
ATGAGATTGAACGGAAAAGAAAAAGG

Alignment

ORF - retro_chof_2231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.52 %
• Parental protein coverage: 90.58 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DHSRVKLQNAENDYINASLVNIEEAQRSYVLTQGPLPNTCCHFWLMVWQQKTKAVVMLNRVVE-KESVKC
          DH..V.LQ.AEND.IN.SLVNI.E.QRSY.LTQG.LPN.CCHFWLM.WQQKTKAV.MLN.VVE....VKC
Retrocopy DHNCVELQIAENDFINTSLVNIKEVQRSYILTQGLLPNMCCHFWLMIWQQKTKAVIMLNQVVELNQVVKC

Parental  AQYWPTKDDREMVFKETGFIVKLLSEDVKSYYTVHLLQLENINSGE-SRTIFHFHYTTWPDFGVPESPAS
          AQY.PTKDD.EMVFKET.F.VKLLSEDVKSY.TV..LQLENINSGE.SR.IFHFH.TTW.DFGVPESPAS
Retrocopy AQY*PTKDDQEMVFKETRFSVKLLSEDVKSYNTVYRLQLENINSGE<SRIIFHFHHTTWTDFGVPESPAS

Parental  FLNFLFKVRESGSLNPEHGPAVVHCSAGIGRSGTFSLVDTCLVLMEQGDDINIKQVLLNMRKYRMGLIQT
          FLNF.FKVRESGSLN.EH.PAVVH.SAGIG.SGTFSLVDTCLVLME.GDDINIK.VL..M.KY.MGLIQT
Retrocopy FLNFSFKVRESGSLNSEHRPAVVHSSAGIGQSGTFSLVDTCLVLMEKGDDINIKKVLPKMKKYQMGLIQT

Parental  PDQLRFSYMAILEGGKFIKGDSNIQKQWKELSK-EDSHAFDLSPTKIMTEKYNGNRIVLDEEKLAGDRCT
          PDQLR.SYMAILEG.KFIKGDSNI.KQ.KE.SK...S..FDLSPTKIM.EKYNGNRIVL.EEKLAGDRC.
Retrocopy PDQLRISYMAILEGAKFIKGDSNIDKQ*KEHSK*YLSPGFDLSPTKIMIEKYNGNRIVLEEEKLAGDRCK

Parental  GLSSKTQDTVEENSESVLRKRIREDRRANTAQKVQQMKQRLNETERKRKR
          GLSSK.QDTVEENSESVL.K.I.EDRRANTAQ..QQMKQR.NE.ERKRKR
Retrocopy GLSSKMQDTVEENSESVLWKHI*EDRRANTAQ*MQQMKQRPNEIERKRKR

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_2231 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000867	1 retrocopy	retro_chof_2231 ,
Callithrix jacchus	ENSCJAG00000005102	1 retrocopy	retro_cjac_1577,
Dasypus novemcinctus	ENSDNOG00000016588	1 retrocopy	retro_dnov_1466,
Erinaceus europaeus	ENSEEUG00000005636	1 retrocopy	retro_eeur_370,
Echinops telfairi	ENSETEG00000005577	2 retrocopies	retro_etel_1743, retro_etel_1942,
Homo sapiens	ENSG00000175354	2 retrocopies	retro_hsap_1186, retro_hsap_480,
Gorilla gorilla	ENSGGOG00000010259	2 retrocopies	retro_ggor_453, retro_ggor_925,
Loxodonta africana	ENSLAFG00000011818	1 retrocopy	retro_lafr_701,
Macropus eugenii	ENSMEUG00000005156	1 retrocopy	retro_meug_653,
Monodelphis domestica	ENSMODG00000021422	1 retrocopy	retro_mdom_1225,
Nomascus leucogenys	ENSNLEG00000009074	3 retrocopies	retro_nleu_2112, retro_nleu_351, retro_nleu_894,
Otolemur garnettii	ENSOGAG00000028605	1 retrocopy	retro_ogar_3429,
Pongo abelii	ENSPPYG00000008983	3 retrocopies	retro_pabe_1077, retro_pabe_1144, retro_pabe_989,
Pan troglodytes	ENSPTRG00000009884	2 retrocopies	retro_ptro_361, retro_ptro_813,