RetrogeneDB ID: retro_pabe_1077

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13_random:2224755..2225847(+)
• 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_1077
CCGCCATACTTGGAAATTCGAAATGAGTCCCATGACTATCTTCATAGAGTGGCCAAGTTTCCAGAAAACAGAAATCGAAA
TAGATACAGAGATGTAAGCCCATATGATCACAGTCGTGTTAAACTGCAAAATGCTGAGAATGATTATATTAATGCCAGCT
TAGTTGACATAGAAGAGGCACAAAGGAGTTACATCTTAACACAGGGTCCACTTCCTAACATGTGCTGCCATTTCTGGCTT
ACAGTTTGGCAGCAGAAGACCAAAGCAGTTGTTGTGCTGAACTGCATTGTGGAGAAAGAATCGGTTAAATGTGCACAGTA
CTGGCCAACAGATGACCAAAAGATGCTGTTTAAAGAAACAGGATTCAGTGTGAAGCTTTCAGAAGATGTGAAGTCATATT
ACACAGTACATCTACTACGATTAGAAAATATCAATAGTGGTGAAACCAGAAAATATCTCACTTTCATTATACTACCTGGC
CAGATTTTGGAGTCCCTGAATCACCAGCTTCATTTCTCAATTTCTTGTTTAAAGGGAGAGATTCTGGCTCCACTGATCAT
GGGCCTGCAGTGATCCATTGTAATGAAGGCACTGGGTGCTCGGGCACCTTCTCTTTGGTAGACACTTGTCTTGTTTTGAT
GGGAAAAGGAGATTATATTAACATTAAACAAGTGTTGTTGAACACGAGAAAATACCGAATGGGTCTTATTCAGACCCCAG
ATCAACTGAGATTCTCATACATGGCTATAATAGAAGGAGCAAAATGTATAAAGGTAGATTCTAGTATACAGAAACGGTGG
AAAGAATTTTCTAAGGAAAACTTAGCTCCTGCTTTTGATCATTAACCAGACAAAATAATGACTGAAAAATACAATGGGAA
CAGAATTGGTCTAGAAGAAGAAAAACTGACAGGTGACCGATGTACAGTAAATGCAAGATACAATGGAAGAGAACAGTGAG
AATGCTCTACGGAAACATATTCTAGAGGACAGAAAGGCCACCACAGCTCAGAAGGTGCAGCAGATGAAACAGAGGCTAAA
TGAGAACGAACGAAAAAGAAAAAGGCCAAGATAGACACCTAATATTCATGAC

Alignment

ORF - retro_pabe_1077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.86 %
• Parental protein coverage: 94.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGP
          P.YLEIRNESHDY.HRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGP
Retrocopy PPYLEIRNESHDYLHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGP

Parental  LPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLL
          LPN.CCHFWL.VWQQKTKAVV.LN.IVEKESVKCAQYWPTDDQ.MLFKETGFSVK.LSEDVKSYYTVHLL
Retrocopy LPNMCCHFWLTVWQQKTKAVVVLNCIVEKESVKCAQYWPTDDQKMLFKETGFSVK-LSEDVKSYYTVHLL

Parental  QLENINSGETR-TISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSL
          .LENINSGETR..ISHFHYTTWPDFGVPESPASFLNFLFK.R.SGS...DHGPAVIHC..G.G.SGTFSL
Retrocopy RLENINSGETR<KISHFHYTTWPDFGVPESPASFLNFLFKGRDSGS--TDHGPAVIHCNEGTGCSGTFSL

Parental  VDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKEDLS
          VDTCLVLM.KGD.INIKQVLLN.RKYRMGLIQTPDQLRFSYMAIIEGAKCIK.DSSIQKRWKE.SKE.L.
Retrocopy VDTCLVLMGKGDYINIKQVLLNTRKYRMGLIQTPDQLRFSYMAIIEGAKCIKVDSSIQKRWKEFSKENLA

Parental  PAFDHSPNKIMTEKFNGNRIGLEEEKLTGDRCTG-LSSKMQDTVEENSESALRKRIREDRKATTAQKVQQ
          PAFDH.P.KIMTEK.NGNRIGLEEEKLTGDRCT......M....E....................Q..Q.
Retrocopy PAFDH*PDKIMTEKYNGNRIGLEEEKLTGDRCTV>MQDTMEENSENALRKHILEDRKATTAQKVQQMKQR

Parental  MKQRLNENERKRKRPRLTD
          .........R.R..P...D
Retrocopy LNENERKRKRPR*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	0.00 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_1077 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1077 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1077 has 0 orthologous retrocopies within eutheria group .

---

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,