RetrogeneDB ID: retro_ptro_813

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:30167530..30168667(+)
• Located in intron of: None

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_813
ATGCCCACCATCATTGAGCGGGAGTTCGAGGAGTTGGATGCTCAGCATCGCTGGCAGCTGCCGTACTTGGAAATTCGAAA
TGAGTCCCATGACTATCTTCATAGAGTGGCCAAGTTTCCAGAAAACAGAAATCGAAATAGATACAGAGATGTAAGCCCAT
ATGATCACAGTCGTGTTAAACTGCAAAATACTGAGAATGATTATATTAATGCCAGCTTAGTTGACATAGAAGAGGCATGA
AGGAGTTACATCTTAACACTGGGTCCACTTCCTAACATGTGCTGCCATTTCTGGCTTACGGTTTGGCAGCAGAAGACCAA
AGCAGTTGTTGTGCTGAACCGCATTGTGGAGAAAGAATCGGTTAAATGTGCGCAGTACTGGCCAACAGATGACCAAAAGA
TGCTGTTTAAAGAAACGGGATTCAATGTGAAGCTCTTTCAGAAGATGTGAAGTCATATTACACAGTACATCTACTACGAT
TAGAAAATATCAATAGTGGTGAAACCAGAACAATATCTCACTTGCATTATACGACCTGGCCAGATTTTGGAGTCCCTGAA
TCACCAGCTTCATTTCTCAATTTCTTGTTGAAAGTGAGAGAATCTGGCTCCTTGAACCCTGACCATGGGCCTGCAGTGAT
CCATTGTAGCGAAGGCACTGGGTGCTCGGGCACCTTCTCTCTGGTAGACGCTTGTCTTGTTTTGATGGGAAAAGGAGATT
ATATTAACATTAAACAAGTGTTATTGAACATGAGAAAATACTGAATGGGTCTTATTCAGACCCCAGATCAACTGAGATTC
TCATACATGGCTATAATAGAAGGAGCAAAATGTATAAAGGTAGATTCTAGTATACAGAAACGGTGGAAAGAATTTTCTAA
GGAAAACTTAGCTCCTGCTTTTGATCATTCACCAAACAAAATAATGACTGAAAAATACAATGGGAACAGAATTGGTCTAG
AAGAAGAAAAACTGACAGGTGACCGATGTACAGTAAATGCAAGATACAATGGAAGAGAACAGTGAGAATGCTCTACGGAA
ACATATTCTAGAGGACAGAAAGGCCACCACAGCTCAGAAGGTGCAGCAGATGAAACAGAGGCTAAATGAGAATGAACAAA
AAAGAAAAAGGCCAAGA

Alignment

ORF - retro_ptro_813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.95 %
• Parental protein coverage: 91.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYIN
          MPT.IEREFEELD.Q.RWQ..YLEIRNESHDY.HRVAKFPENRNRNRYRDVSPYDHSRVKLQN.ENDYIN
Retrocopy MPTIIEREFEELDAQHRWQLPYLEIRNESHDYLHRVAKFPENRNRNRYRDVSPYDHSRVKLQNTENDYIN

Parental  ASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQELLFKETG
          ASLVDIEEA.RSYILT.GPLPN.CCHFWL.V..........LNRIVEKESVKCAQYWPTDDQ..LFKETG
Retrocopy ASLVDIEEA*RSYILTLGPLPNMCCHFWLTVXXXXXXXXXXLNRIVEKESVKCAQYWPTDDQKMLFKETG

Parental  FSVKL-LSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDH
          F.VKL.LSEDVKSYYTVHLL.LENINSGETRTISH.HYTTWPDFGVPESPASFLNFL.KVRESGSLNPDH
Retrocopy FNVKL<LSEDVKSYYTVHLLRLENINSGETRTISHLHYTTWPDFGVPESPASFLNFLLKVRESGSLNPDH

Parental  GPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCI
          GPAVIHCS.G.G.SGTFSLVD.CLVLM.KGD.INIKQVLLNMRKY.MGLIQTPDQLRFSYMAIIEGAKCI
Retrocopy GPAVIHCSEGTGCSGTFSLVDACLVLMGKGDYINIKQVLLNMRKY*MGLIQTPDQLRFSYMAIIEGAKCI

Parental  KGDSSIQKRWKELSKEDLSPAFDHSPNKIITEKYNGNRIGLEEEKLTGDRYTG-LSSKMQDTMEENSESA
          K.DSSIQKRWKE.SKE.L.PAFDHSPNKI.TEKYNGNRIGLEEEKLTGDR.T......M....E......
Retrocopy KVDSSIQKRWKEFSKENLAPAFDHSPNKIMTEKYNGNRIGLEEEKLTGDRCTV>MQDTMEENSENALRKH

Parental  LRKRIREDRKATTAQKVQQMKQRLNENERKR
          ..............Q..Q..........R.R
Retrocopy ILEDRKATTAQKVQQMKQRLNENEQKRKRPR

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	0.04 RPM	4.74 RPM
SRP007412_cerebellum	0.11 RPM	12.69 RPM
SRP007412_heart	0.09 RPM	4.43 RPM
SRP007412_kidney	0.03 RPM	9.62 RPM
SRP007412_liver	0.03 RPM	12.70 RPM
SRP007412_testis	0.21 RPM	7.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_ptro_813 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DC522310	30167534	30167922	95.3	347	13	329

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_813 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1186
Pongo abelii	retro_pabe_989

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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 ,