RetrogeneDB ID: retro_nleu_2112

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397329.1:3564914..3565747(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSNLEG00000009074
• Aliases: None
• Description: Tyrosine-protein phosphatase non-receptor type [Source:UniProtKB/TrEMBL;Acc:G1RCW5]

Sequence

>retro_nleu_2112
ATGCTCACCATCATTGAGCGGGAGTTCAAGGAATTGGATGCTCAGCATCGCTGGCAGCCGCCGTACTTGGAAATTCGAAA
TGAGTCCCATGACTATCTTCATAGAGTGGCCAAGTTTCCAGAAAACAGAAATCGAAATAGATACAGAGATGTAAGCCCAT
ATGATCACAGTCGTGTTAAACTGCAAAATGCTGAGAATGATTATATTAATGCCAGCTTAGTTGACACAGAAGAGGCACAA
AGGAGTTACATCTTAACACAGGGTCCACTTCCTAACATGTGCTGCCATTTCTGGCTTACGGTTTGGCAGCAGAAGACCAA
AGCAGTTGTTGTGCTGAACCGCACTGTGGAGAAAGAATCGGTTAAATGTGCACAGTACTGGCCAACAGATGACCAAAAGA
TGCTGTTTAAAGACACAGGATTCAGTGTGAAGCTCTTTCAGAAGATGTGAAGTCATATTACACAGTACATCTACTACGAT
TAGAAAATATCAATAGTGGTGAAACCAGAACAATATCTCACTTTCATTATACTACCTGGCCAGATTTTGGAGCCCCTGAA
TCACCAGCTTCATTTCTCAATTTCTTGTTTAAAGTGAGAGAATCTGGCTCCTTGAACCCTGACCATGGGCCTGCAGTGAT
CCATTGTAGTGAAGGCACTGGGTGCTCGGGCACCTTCTCTCTGGTAGACACTTGTCTTGTTTTGATGGGAAAAGGAGATT
ATATTAACATTAAACAAGTGTTACTGAACATGAGAAAATACCGAATGGGTCTTATTCAGACCCCAGATCAACTGAGATTC
ACATATATGGCTATAATAGCATGTATAATATGC

Alignment

ORF - retro_nleu_2112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.3 %
• Parental protein coverage: 66.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPTSIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYIN
          M.T.IEREF.ELD.Q.RWQP.YLEIRNESHDY.HRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYIN
Retrocopy MLTIIEREFKELDAQHRWQPPYLEIRNESHDYLHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYIN

Parental  ASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETG
          ASLVD.EEAQRSYILTQGPLPN.CCHFWL.V................KESVKCAQYWPTDDQ.MLFK.TG
Retrocopy ASLVDTEEAQRSYILTQGPLPNMCCHFWLTVXXXXXXXXXXXXXXXXKESVKCAQYWPTDDQKMLFKDTG

Parental  FSVKL-LSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDH
          FSVKL.LSEDVKSYYTVHLL.LENINSGETRTISHFHYTTWPDFG.PESPASFLNFLFKVRESGSLNPDH
Retrocopy FSVKL<LSEDVKSYYTVHLLRLENINSGETRTISHFHYTTWPDFGAPESPASFLNFLFKVRESGSLNPDH

Parental  GPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKC
          GPAVIHCS.G.G.SGTFSLVDTCLVLM.KGD.INIKQVLLNMRKYRMGLIQTPDQLRF.YMAII....C
Retrocopy GPAVIHCSEGTGCSGTFSLVDTCLVLMGKGDYINIKQVLLNMRKYRMGLIQTPDQLRFTYMAIIACIIC

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2112 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 15 parental genes, and 27 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	ENSNLEG00000000078	5 retrocopies	retro_nleu_1200, retro_nleu_1360, retro_nleu_1654, retro_nleu_522, retro_nleu_561,
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,