RetrogeneDB ID: retro_nleu_894

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397275.1:29366754..29367734(-)
• Located in intron of: ENSNLEG00000015544

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_894
GATCACCGTTGTGTTAAACTGCAAAATGCTGAGAATGATTATATTAATGCCAGCTTAGTTGACATAGAAGAGGCACAAAG
GAGTTACATCTTAACACAGGATCCACTTCCTAACACATGATGCCATTGCTGGCTTATGGTTTGGCAGCAGAAGACCAAAG
CAGTTGTCATGCTGAACCGCACTGTGGAGAAAGAATCGGTTAAATGTGCACAGTACTGGCCAACAGATGACCAAGAGATG
CTGTTTAAAGAAACAGGATTCAGTGTGAAGCTCTTGTCAGAAGATGTGAAGTCGTATTATACAGTACATCTACCACAATT
AGAAAATATCAATAGTGGTGAAATCAGAACAATATCTCACTTTCATTATACTACTTGGCCACATTTTGGAGTCCCTCAAT
CACCAGTTTCATTTCTCAACTTCTTGTTTAAAGTGAGAGAATCTGGCTCCTTGAACCGTGACCACGGACCTGCGGTGATC
CACTGTAGTGCAGGCATTGGACGCTCCAGCACCTTCCCTCTGGTAGACACTTGTCTTGTTTTGATGGAAAAAGGAGATGA
TATTAACATTAAACAAATGTTACTGAACATGAGAAAATTCCGAATGGGTCTTATCTCAGACCCCAGATCAACTGAGATTC
TCATACATGGCTATAATAGAAGGGGCAAAATGTGTAAAGGGAGATTCTAGTATACAGAAACAATGGAAAGAACTTTCTAA
GGAAGACTACCTCCTGCTTTTGATCATTCACCAAACAAAATAATGGCGAAAAATACAATGGGAACAGAATAGGTCTAGAA
GAAGACAAACTGACAGGTGACTGATGTACAGGACTTTCCTCTAAAATGCAAGATACAATGGAGGAGAACAATGAGAGTGT
TCTATGGAAATGTATCTGAGAGGACAGAAAGGCCACCACAGCTCAGAAGGTGCAGCAGATGAAATACAGGCTAAATGAGA
ATGAACGAAAAAGAAAAAGG

Alignment

ORF - retro_nleu_894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.3 %
• Parental protein coverage: 78.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCA
          DH..VKLQNAENDYINASLVDIEEAQRSYILTQ.PLPNT.CH.WLMVWQQKTKAVVMLNR.VEKESVKCA
Retrocopy DHRCVKLQNAENDYINASLVDIEEAQRSYILTQDPLPNT*CHCWLMVWQQKTKAVVMLNRTVEKESVKCA

Parental  QYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLN
          QYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHL.QLENINSGE.RTISHFHYTTWP.FGVP.SP.SFLN
Retrocopy QYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLPQLENINSGEIRTISHFHYTTWPHFGVPQSPVSFLN

Parental  FLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLI-QTPD
          FLFKVRESGSLN.DHGPAVIHCSAGIGRS.TF.LVDTCLVLMEKGDDINIKQ.LLNMRK.RMGLI.QTPD
Retrocopy FLFKVRESGSLNRDHGPAVIHCSAGIGRSSTFPLVDTCLVLMEKGDDINIKQMLLNMRKFRMGLI>QTPD

Parental  QLRFSYMAIIEGAKCIKGDSGIQKRWKELSKED-LSPAFDHSPNKIMT-EKYNGNRIGLEEEKLTGDRCT
          QLRFSYMAIIEGAKC.KGDS.IQK.WKELSKED.L.PAFDHSPNKIM..EKYNGNRIGLEE.KLTGD.CT
Retrocopy QLRFSYMAIIEGAKCVKGDSSIQKQWKELSKED<LPPAFDHSPNKIMA<EKYNGNRIGLEEDKLTGD*CT

Parental  GLSSKMQDTMEENSESALRKRIREDRKATTAQKVQQMKQRLNENERKRKR
          GLSSKMQDTMEEN.ES.L.K.I.EDRKATTAQKVQQMK.RLNENERKRKR
Retrocopy GLSSKMQDTMEENNESVLWKCI*EDRKATTAQKVQQMKYRLNENERKRKR

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_894 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,