RetrogeneDB ID: retro_pabe_989

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:30076867..30078015(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSPPYG00000008983
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 2 [Source:HGNC Symbol;Acc:9650]

Sequence

>retro_pabe_989
ATGCCCACCATCATAGAGCGGGAGTTCGAGGAGTTGGATGCTCAGCATTGCTGGCACCCGCCCTACTTGGAAATTCGAAA
TGAGTCCCATGACTATCTTCATAGAGTGGCCAAGTTTCCAGAAAACAGAAATCGAAATAGATACAGAGATGTAAGCCCAT
ATGATCACAGTCGTGTTAAACTGCAAAATGCTGAGAATGATTATATTAATGCCAGCTTAGTTGACATAGAAGAGGCACAA
AGGAGTTACATCTTAACACAGGGTCCACTTCCTAACATGTGCTGCCATTTCTGGCTTACGGTTTGGCAGCAGAAGACCAA
AGCAGTTGTGCTGAACTGCATTGTGGAGAAAGAATCGGTTAAATGTGCACAGTACTGGCCAACAGATGACCAAAAGATGC
TGTTTAAAGAAACAGGATTCAGTGTGAAGCTCTTTCAGAAGATGTGAAGTCATATTACACAGTACATCTACTACGATTAG
AAAATATCAATAGTGGTGAAACCAGAAAATATCTCACTTTCATTATACTACCTGGCCAGATTTTGGAGTCCCTGAATCAC
CAGCTTCATTTCTCAATTTCTTGTTTAAAGGGAGAGATTCTGGCTCCACTGATCATGGGCCTGCAGTGATCCATTGTAAT
GAAGGCACTGGGTGCTCGGGCACCTTCTCTTTGGTAGACACTTGTCTTGTTTTGATGGGAAAAGGAGATTATATTAACAT
TAAACAAGTGTTGTTGAACAAGAGAAAATACCGAATGGGTCTTATTCAGACCCCAGATCAACTGAGATTCTCATACATGG
CTATAATAGAAGGAGCAAAATGTATAAAGGTAGATTCTAGTATACAGAGACGGTGGAAAGAATTTTCTAAGGAAAACTTA
GCTCCTGCTTTTGATCATTAACCAAACAAAATAATGACTGAAAAATACAATGGGAACAGAATTGGTCTAGAAGAAGAAAA
ACTGACAGGTGACCGATGTACAGTAAATGCAAGATACAATGGAAGAGAACAGTGAGAATGCTCTACGGAAACATATTCTA
GAGGACAGAAAGGCCACCACAGCTCAGAAGGTGCAGCAGATGAAACAGAGGCTAAATGAGAACGAACGAAAAAGAAAAAG
GCCAAGATAGACACCTAATATTCATGAC

Alignment

ORF - retro_pabe_989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.41 %
• Parental protein coverage: 99.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPTTIEREFEEVDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYIN
          MPT.IEREFEE.D.Q..W.P.YLEIRNESHDY.HRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYIN
Retrocopy MPTIIEREFEELDAQHCWHPPYLEIRNESHDYLHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYIN

Parental  ASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETG
          ASLVDIEEAQRSYILTQGPLPN.CCHFWL.VWQQKTKAVV.LN.IVEKESVKCAQYWPTDDQ.MLFKETG
Retrocopy ASLVDIEEAQRSYILTQGPLPNMCCHFWLTVWQQKTKAVV-LNCIVEKESVKCAQYWPTDDQKMLFKETG

Parental  FSVKL-LSEDVKSYYTVHLLQLENINSGETRT-ISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPD
          FSVKL.LSEDVKSYYTVHLL.LENINSGETR..ISHFHYTTWPDFGVPESPASFLNFLFK.R.SGS...D
Retrocopy FSVKL<LSEDVKSYYTVHLLRLENINSGETRK<ISHFHYTTWPDFGVPESPASFLNFLFKGRDSGST--D

Parental  HGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKC
          HGPAVIHC..G.G.SGTFSLVDTCLVLM.KGD.INIKQVLLN.RKYRMGLIQTPDQLRFSYMAIIEGAKC
Retrocopy HGPAVIHCNEGTGCSGTFSLVDTCLVLMGKGDYINIKQVLLNKRKYRMGLIQTPDQLRFSYMAIIEGAKC

Parental  IKGDSSIQKRWKELSKEDLSPAFDHSPNKIMTEKFNGNRIGLEEEKLTGDRCTG-LSSKMQDTVEENSES
          IK.DSSIQ.RWKE.SKE.L.PAFDH.PNKIMTEK.NGNRIGLEEEKLTGDRCT......M....E.....
Retrocopy IKVDSSIQRRWKEFSKENLAPAFDH*PNKIMTEKYNGNRIGLEEEKLTGDRCTV>MQDTMEENSENALRK

Parental  ALRKRIREDRKATTAQKVQQMKQRLNENERKRKRPRLTD
          ...............Q..Q..........R.R..P...D
Retrocopy HILEDRKATTAQKVQQMKQRLNENERKRKRPR*TPNIHD

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.21 RPM
SRP007412_cerebellum	0.00 RPM	7.17 RPM
SRP007412_heart	0.06 RPM	2.11 RPM
SRP007412_kidney	0.00 RPM	3.41 RPM
SRP007412_liver	0.00 RPM	7.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_989 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_989 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_989 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1186
Pan troglodytes	retro_ptro_813

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 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	ENSPPYG00000004976	4 retrocopies	retro_pabe_2205, retro_pabe_2535, retro_pabe_2825, retro_pabe_3336,
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,