RetrogeneDB ID: retro_ptro_1464

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:8841839..8842948(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK6
• Ensembl ID: ENSPTRG00000020224
• Aliases: None
• Description: None

Sequence

>retro_ptro_1464
GCTGTAGACGATGACTGTGATAAAAGAGAATCCATCAAGAAAATTCTCCTTACTGATCCCCAGAGTGTCAAAAATGCTCT
ACATGAAATCAAAATTATTAGAAGATTTGACATCGTGACATTGTGAAAGTGTTTGAAATTCCTAGTACCAGTGGAAGCCA
ATTAACAAACAATGTGAACTCTCTTACCAAACTTAACAGTATTTACATTTTTCAGAATTACATGGAGACAGACTTGGCTA
ATATGATGGAGGAGGGCCCTTTACTGGAAAAGCATGCCAGACTTTTCATGTATCAGCTGCTAAGGTGGCTTAAGTATTCA
CTCTGCAAGTGTATTGCCCAGATATCTCAAACCAACTAATCTTTTCATTAATACTGAAGACATGATGCTGAAGATAGGGG
ACTTTTGTCTTGCACAAATCATGGATCCTCATTATTCCCATAAGGATCATCTCTCTGAAGGACTGGTAACTAAATGTACA
GATCTCCACATCTTTTACATTCTTCTAATAGTTATAGTAAAGCCATTGACATGTGGGCTGCAGGCCACATCTTTGCTGAA
ATGCTGACTGGTAAAACCGTTTTTGCAGGTGCACGTGAACTCGAACAGATGCAGCTGATTTTAGAATCTAGTCCTGTTAT
ACATGAGGAAGATCATCAGGAGCTTCTCAGTGTAATTCCAGTTTACATTAGAAATGAAATGACTGAACCACAGAAACCTT
TAACTCAGCTGCTTCAGGGAATTAGCTGAGAAGCACTGGATCTCCTGGAACAAATTTTGACATTTATCCCTACAGATGGG
TTAACAGCAGAAGAAGCGCTCTCCCATCATTACATGAGCATATATTATTTTCCAACGGATGAGCCAATTTCAAGTCATCT
TTTTCATATTGAAGATGAAGTTTATGATATTTTGCTTATGGATGAAACTCACAGTCACATTTATAACTGGGAAAGGTATG
ATTGTTAGTTTTCAGCGCATGATTGGCCTATACATAACAACTTTGGTATTGATGAAGTTCTGCTTGACCCGAGAGCTCTG
TCTGATATCACTGATGAAGAAGTACAAGTTGATCCCTGAAAATATTTGGATGGACATTCGGAAAAGTAT

Alignment

ORF - retro_ptro_1464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.59 %
• Parental protein coverage: 51.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLD-HDNIVKVFEILGPSGSQLTDDVGSLTELNSVY
          AVD.DCDKR..IKKI.LTDPQSVK.AL.EIKIIRR.D.H..IVKVFEI...SGSQLT..V.SLT.LNS.Y
Retrocopy AVDDDCDKRESIKKILLTDPQSVKNALHEIKIIRRFD<HRDIVKVFEIPSTSGSQLTNNVNSLTKLNSIY

Parental  IVQEYMETDLANVLEQGPLLEEHARLFMYQLLR-GLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGL
          I.Q.YMETDLAN..E.GPLLE.HARLFMYQLLR.GL..IHSA.VL.R.LKP.NLFINTED..LKIGDF.L
Retrocopy IFQNYMETDLANMMEEGPLLEKHARLFMYQLLR>GLS-IHSASVLPRYLKPTNLFINTEDMMLKIGDFCL

Parental  ARIMDPHYSHKGHLSEGLVTK-WYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQL
          A.IMDPHYSHK.HLSEGLVTK..YRSP.LL.S.N.Y.KAIDMWAAG.IFAEMLTGKT.FAGA.ELEQMQL
Retrocopy AQIMDPHYSHKDHLSEGLVTK<MYRSPHLLHSSNSYSKAIDMWAAGHIFAEMLTGKTVFAGARELEQMQL

Parental  ILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREALDFLEQILTFSPMDRLTAEEALSH
          ILES.PV.HEED.QELLSVIPVYIRN.MTEP.KPLTQLL.GIS.EALD.LEQILTF.P.D.LTAEEALSH
Retrocopy ILESSPVIHEEDHQELLSVIPVYIRNEMTEPQKPLTQLLQGIS*EALDLLEQILTFIPTDGLTAEEALSH

Parental  PYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSHIYNWERYHDCQFSEHDWPVHNNFDIDEVQLDPR
          .YMSIY.FP.DEPISSH.FHIEDEV.DILLMDETHSHIYNWERY.DC.FS.HDWP.HNNF.IDEV.LDPR
Retrocopy HYMSIYYFPTDEPISSHLFHIEDEVYDILLMDETHSHIYNWERY-DC*FSAHDWPIHNNFGIDEVLLDPR

Parental  ALSDVTDEEEVQVDPRKYLDGDREKY
          ALSD.TD.EEVQVDP.KYLDG..EKY
Retrocopy ALSDITD-EEVQVDP*KYLDGHSEKY

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	39.31 RPM
SRP007412_cerebellum	0.00 RPM	72.23 RPM
SRP007412_heart	0.00 RPM	14.86 RPM
SRP007412_kidney	0.00 RPM	25.99 RPM
SRP007412_liver	0.00 RPM	34.34 RPM
SRP007412_testis	0.00 RPM	164.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1464 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1464 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2519
Gorilla gorilla	retro_ggor_1571
Pongo abelii	retro_pabe_1853

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000962	1 retrocopy	retro_cjac_2633,
Homo sapiens	ENSG00000069956	2 retrocopies	retro_hsap_1257, retro_hsap_2519,
Gorilla gorilla	ENSGGOG00000004003	1 retrocopy	retro_ggor_1571,
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138, retro_mdom_63,
Nomascus leucogenys	ENSNLEG00000006476	2 retrocopies	retro_nleu_1441, retro_nleu_2095,
Otolemur garnettii	ENSOGAG00000030786	1 retrocopy	retro_ogar_1827,
Pongo abelii	ENSPPYG00000006482	2 retrocopies	retro_pabe_1853, retro_pabe_3322,
Pan troglodytes	ENSPTRG00000008904	1 retrocopy	retro_ptro_2845,
Pan troglodytes	ENSPTRG00000020224	3 retrocopies	retro_ptro_1464 , retro_ptro_2743, retro_ptro_3045,
Sarcophilus harrisii	ENSSHAG00000017091	1 retrocopy	retro_shar_445,
Tupaia belangeri	ENSTBEG00000007876	2 retrocopies	retro_tbel_1879, retro_tbel_2946,
Tursiops truncatus	ENSTTRG00000016253	2 retrocopies	retro_ttru_322, retro_ttru_75,