RetrogeneDB ID: retro_ptro_361

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:157261417..157262394(-)
• Located in intron of: ENSPTRG00000001722

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSPTRG00000009884
• Aliases: None
• Description: Tyrosine-protein phosphatase non-receptor type [Source:UniProtKB/TrEMBL;Acc:H2QEA6]

Sequence

>retro_ptro_361
GATCACAGTTGTGTTAAACTGCAAAATGCTGAGAATGATTATATTAATGCCAGCTTAGTTGACACAGAAGAGGACAAAGG
AGTTACATCTTAACACAGGGTCCACTTCCTAACACATGCTGCCATTTCTGGCTTATGGTTTGGCAGCAGAAGACCAAAGC
AGTTGTCATGCTGAACCGCATTATGGAGAAAGAATTGGTTAAATGTGCACAGTACTGGCCAACAGATGACCAAGAGATGC
TGTTTAAAGAAACAGGATTCAGTGTGAAGCTCTTGTCAGAAGATGTGAAGTCGTATTATACAGTACATCTACCACAATTA
GAAAATATCAATAGTGGTGAAACCAGAACAATATCTCACTTTCATTATACTACTTGGCCAGATTTTGGAGTCCCTCAATC
ACCAGCTTCATTTCTCAATTTCTTGTTTAAAGTGAGAGAATCTGGCTCCTTGAACCCTGACCATGGACCTGTGGTGATCC
ACCGTAGTGCAGGCACTGGACGCTCCAGCACCTTCTCTCTGGTAGACACTTGTCTTGTTTTGTGGAAAAAGGAGATGATA
TTAACATTAAACAAGTGTTACTGAACGTAAGAAAATTCCGAATGGGTCTTATCTCAGACCCCAGATCAACTGAGATTCTC
ATACATGGCTATAATAGAAGGAGCAAAATGTGTAAAGGGAGATTCTAGTATACAGAAACGATGGAAAGAACTTTCTAAGG
AAGACTACCTCCTGCTTTTGATCATTCACCAAACAAAATAATGACTGAAAAATACAATAGGAACAGAATAGGTCTAGAAG
AAGAAAAACTGACAGGTGACTGACACACAGGACTTTCCTCTAAAAGGCAAGATACAATAGAGGAGAACAATGAGAGTGTT
CTACGGAAACGTATGTGAGGACAGAAAGGCCACCACAGCTCAGAAGGTGCAGCAGATGAAACAGAGGCTAAATGAGAATG
AACGAAAAAGAAAAAGG

Alignment

ORF - retro_ptro_361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.84 %
• Parental protein coverage: 78.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DHSRVKLQNAENDYINASLVDIEE-AQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKC
          DHS.VKLQNAENDYINASLVD.EE..QRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRI.EKE.VKC
Retrocopy DHSCVKLQNAENDYINASLVDTEE<GQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIMEKELVKC

Parental  AQYWPTDDQELLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFL
          AQYWPTDDQE.LFKETGFSVKLLSEDVKSYYTVHL.QLENINSGETRTISHFHYTTWPDFGVP.SPASFL
Retrocopy AQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLPQLENINSGETRTISHFHYTTWPDFGVPQSPASFL

Parental  NFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVL-MEKGDDINIKQVLLNMRKYRMGLI-QT
          NFLFKVRESGSLNPDHGP.VIH.SAG.GRS.TFSLVDTCLVL..EKGDDINIKQVLLN.RK.RMGLI.QT
Retrocopy NFLFKVRESGSLNPDHGPVVIHRSAGTGRSSTFSLVDTCLVL<VEKGDDINIKQVLLNVRKFRMGLI>QT

Parental  PDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKED-LSPAFDHSPNKIITEKYNGNRIGLEEEKLTGDRY
          PDQLRFSYMAIIEGAKC.KGDSSIQKRWKELSKED.L.PAFDHSPNKI.TEKYN.NRIGLEEEKLTGD..
Retrocopy PDQLRFSYMAIIEGAKCVKGDSSIQKRWKELSKED<LPPAFDHSPNKIMTEKYNRNRIGLEEEKLTGD*H

Parental  TGLSSKMQDTMEENSESALRKRI-REDRKATTAQKVQQMKQRLNENERKRKR
          TGLSSK.QDT.EEN.ES.LRKR........T.....Q.....LNENERKRKR
Retrocopy TGLSSKRQDTIEENNESVLRKRM>EDRKATTAQKVQQMKQR-LNENERKRKR

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	0.16 RPM	4.74 RPM
SRP007412_cerebellum	0.29 RPM	12.69 RPM
SRP007412_heart	0.32 RPM	4.43 RPM
SRP007412_kidney	0.73 RPM	9.62 RPM
SRP007412_liver	1.08 RPM	12.70 RPM
SRP007412_testis	0.53 RPM	7.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_361 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_361 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_361 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 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	ENSPTRG00000004601	1 retrocopy	retro_ptro_37,
Pan troglodytes	ENSPTRG00000009884	2 retrocopies	retro_ptro_361 , retro_ptro_813,