RetrogeneDB ID: retro_meug_653

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold152407:2071..2731(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSMEUG00000005156
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 2 [Source:HGNC Symbol;Acc:9650]

Sequence

>retro_meug_653
GAAGACGTACACAATGACTATATAAATGCCAGCTATGTGGTGATGGAGGAGGCCCAGCGGAGCTATATCCTGGCACAAGG
TCCGCTGCCCAACACATGCGGTCACTTCTGGCTCATGGTATGGCAGCAGAACAGCAGGGCCGTGATTATGCTCAACCAGT
TGGTGGAGAAGGAGTCCATCAAGTGCTCCCAGTACTGGCCCCCCCACCAGGGCCAGACCCTCCTCTTTGAGGAGATTGGC
ATCAGGGTGCACATGCTGGGGGAGGAGGTGAGAGCCTTCCACAGGGTCCGCCACCTGAAGCTGGAAAGTGTGCTGAGTGG
GGAGTTCAGGGATATTTCCCACTTCCAATACACCAGCTGGCCCGACTTCGGGGTGCCTGAATCCCCGGGCCCTTTCCTTG
CTTTCCTTTTCATGGTGTGGGAGTCTGGCTTCCTAAACTGTGAGGAGGGGCCTGCGGTTATCCACTGCAGTGCCGGCATT
GGCCGCTCAGGCACCTTTGCTCTGATTGATTCCTGCCTGGTCCTGATGGGAAAGAGAGAGAACCCCTTTTCCCTGAATAT
CAGACAGGTATTGGTGTCTCTGAGAAAGTACCGGATGAGACTTATTAAGACCCCAGAACAGCTGAGATTCTCATACATGG
CTGTCATTGAAGGGCAAAAG

Alignment

ORF - retro_meug_653 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.55 %
• Parental protein coverage: 75.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QNTENDYINASFVAIEEAQRNYILTQGPLPNTCCHFWLMVWQQKSKAVVMLNRIVEKDSLKCAQYWPQKE
          ....NDYINAS.V..EEAQR.YIL.QGPLPNTC.HFWLMVWQQ.S.AV.MLN..VEK.S.KC.QYWP...
Retrocopy EDVHNDYINASYVVMEEAQRSYILAQGPLPNTCGHFWLMVWQQNSRAVIMLNQLVEKESIKCSQYWPPHQ

Parental  EKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTSGETRIISHFHYTTWPDFGVPESPASFLNFLFKVR
          .....FE..........E.......VR.L.LE...SGE.R.ISHF.YT.WPDFGVPESP..FL.FLF.V.
Retrocopy GQTLLFEEIGIRVHMLGEEVRAFHRVRHLKLESVLSGEFRDISHFQYTSWPDFGVPESPGPFLAFLFMVW

Parental  ESGSLSAEHGPAIIHCSAGIGRSGTFSLVDTCLVLMEKRDDPFSVDIKQVLLNMRKYRMGLIQTPDQLRF
          ESG.L..E.GPA.IHCSAGIGRSGTF.L.D.CLVLM.KR..PFS..I.QVL...RKYRM.LI.TP.QLRF
Retrocopy ESGFLNCEEGPAVIHCSAGIGRSGTFALIDSCLVLMGKRENPFSLNIRQVLVSLRKYRMRLIKTPEQLRF

Parental  SYMAVIEGAK
          SYMAVIEG.K
Retrocopy SYMAVIEGQK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_653 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_653 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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,