RetrogeneDB ID: retro_hsap_480

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:178715820..178716818(-)
• Located in intron of: ENSG00000116191

Retrocopy information

• Ensembl ID: ENSG00000228196
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSG00000175354
• Aliases: PTPN2, PTN2, PTPT, TC-PTP, TCELLPTP, TCPTP
• Description: protein tyrosine phosphatase, non-receptor type 2 [Source:HGNC Symbol;Acc:9650]

Sequence

>retro_hsap_480
GATCACAGTTGTGTTAAACTGCAAAATGCTGAGAATGATTATATTAATGCCAGCTTAGTTGACATAGAAGAGGACAAAGG
AGTTACATCTTAACACAGGGTCCACTTCCTAACACATGCTGCCATTTCTGGCTTATGGTTTGGCAGCAGAAGACCAAAGC
AGTTGTCATGCTGAACCGCATTATGGAGAAAGAATTGGTTAAATGTGCACAGTACTGGCCAACAGATGACCAAGAGATGC
TGTTTAAAGAAACAGGATTCAGTGTGAAGCTCTTGTCAGAAGATGTGAAGTCGTATTATACAGTACATCTACCACAATTA
GAAAATATCAATAGTGGTGAAACCAGAACAATATCTCACTTTCATTATACTACTTGGCCAGATTTTGGAGTCCCTCAATC
ACCAGCTTCATTTCTCAATTTCTTGTTTAAAGTGAGAGAATCTGGCTCCTTGAACCCTGACCATGGACCTGTGGTGATCC
ACCGTAGTGCAGGCACTGGACGCTCCAGCACCTTCTCTCTGGTAGACACTTGTCTTGTTTTGATGGAAAAAGGAGATGAT
ATTAACATTAAACAAGTGTTACTGAACATAAGAAAATTCCAAATGGGTCTTATCTCAGACCCCAGATCAACTGAGATTCT
CATACATGGCTATAACAGAAGGAGCAAAATGTGTAAAGGGAGATTCTAGTATACAGAAACGATGGAAAGAACTTTCTAAG
GAAGACTACCTCCTGCTTTTGATCATTCACCAAACAAAATAATGACTGAAAAATACAATAGGAACAGAATAGGTCTAGAA
GAAGAAAAACTGACAGGTGACTGACGTACAGGACTTTCCTCTAAAATGCAAGATACAATGGAGGAGAACAATGAGAGTGT
TCTACGGAAACGTATGTGAGAGGACAGAAAGGCCACCACAGCTCAGAAGGTGCAGCAGATGAAATAGAGGCTAAATGAGA
ATGAACGAAAAAGAAAAAGGCCAAGATTGACAGATACC

Alignment

ORF - retro_hsap_480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.96 %
• Parental protein coverage: 86.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DHSRVKLQNAENDYINASLVDIEE-AQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKC
          DHS.VKLQNAENDYINASLVDIEE..QRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRI.EKE.VKC
Retrocopy DHSCVKLQNAENDYINASLVDIEE<GQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIMEKELVKC

Parental  AQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFL
          AQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHL.QLENINSGETRTISHFHYTTWPDFGVP.SPASFL
Retrocopy AQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLPQLENINSGETRTISHFHYTTWPDFGVPQSPASFL

Parental  NFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLI-QTP
          NFLFKVRESGSLNPDHGP.VIH.SAG.GRS.TFSLVDTCLVLMEKGDDINIKQVLLN.RK..MGLI.QTP
Retrocopy NFLFKVRESGSLNPDHGPVVIHRSAGTGRSSTFSLVDTCLVLMEKGDDINIKQVLLNIRKFQMGLI>QTP

Parental  DQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKED-LSPAFDHSPNKIMTEKYNGNRIGLEEEKLTGDRCT
          DQLRFSYMAI.EGAKC.KGDSSIQKRWKELSKED.L.PAFDHSPNKIMTEKYN.NRIGLEEEKLTGD..T
Retrocopy DQLRFSYMAITEGAKCVKGDSSIQKRWKELSKED<LPPAFDHSPNKIMTEKYNRNRIGLEEEKLTGD*RT

Parental  GLSSKMQDTMEENSESALRKRIREDRKATTAQKVQQMKQRLNENERKRKRPRLTDT
          GLSSKMQDTMEEN.ES.LRKR..EDRKATTAQKVQQMK.RLNENERKRKRPRLTDT
Retrocopy GLSSKMQDTMEENNESVLRKRM*EDRKATTAQKVQQMK*RLNENERKRKRPRLTDT

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
bodymap2_adipose	0.00 RPM	22.36 RPM
bodymap2_adrenal	0.31 RPM	53.96 RPM
bodymap2_brain	0.02 RPM	16.55 RPM
bodymap2_breast	0.00 RPM	23.35 RPM
bodymap2_colon	0.00 RPM	23.03 RPM
bodymap2_heart	0.00 RPM	10.91 RPM
bodymap2_kidney	0.08 RPM	24.47 RPM
bodymap2_liver	0.08 RPM	12.53 RPM
bodymap2_lung	0.00 RPM	43.25 RPM
bodymap2_lymph_node	0.00 RPM	54.88 RPM
bodymap2_ovary	0.10 RPM	48.85 RPM
bodymap2_prostate	0.00 RPM	28.87 RPM
bodymap2_skeletal_muscle	0.02 RPM	12.09 RPM
bodymap2_testis	0.00 RPM	35.31 RPM
bodymap2_thyroid	0.15 RPM	26.36 RPM
bodymap2_white_blood_cells	0.00 RPM	55.32 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_480 was not detected

EST

No EST(s) were mapped for retro_hsap_480 retrocopy.

TSS

No TSS is located nearby retro_hsap_480 retrocopy 5' end.

Lab

retro_hsap_480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_480 has 0 orthologous retrocopies within eutheria group .

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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 ,
Homo sapiens	ENSG00000179295	5 retrocopies	retro_hsap_2823, retro_hsap_3061, retro_hsap_3302, retro_hsap_3670, retro_hsap_4062,
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	ENSPTRG00000009884	2 retrocopies	retro_ptro_361, retro_ptro_813,