RetrogeneDB ID: retro_pabe_1853

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:22498302..22499526(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK6
• Ensembl ID: ENSPPYG00000006482
• Aliases: None
• Description: mitogen-activated protein kinase 6 [Source:HGNC Symbol;Acc:6879]

Sequence

>retro_pabe_1853
CTGGCAGAGAAAGCTGAAAGTCTCATGAACATTCACGGTTTTGATCTGGGCACTGGATATATGAACTTAAAACCATTGGA
TAGTGGAGGCAACAGCTTGTTTTTTTTCTGCTGTAGACAATGACTGTGATAAAAGAGAATCCATCAAGAAAATTCTCCTT
ACTGATCCCCAGAGTGTCAAAAATGCTCTACATGAAATCAAAATTATTAGAAGATTTGACATCGTGACATTGTGAAAGTG
TTTGAAATTCCTAGTACCAGTGGAAGCCAATTAACAAACAATGTGAACTCTCTTACCAAACTTAACAGTATTTACATTTT
TCAGAATTACATGGAGACAGACTTGGCTAATATGCTGGAGGAGGGCCCTTTACTGGAAAAGCATGCCAGACTTTTCATGT
ATCAGCTGCTAAGGTGGCTTAAGTACATTCACTCTGCAAATGTATTGCCCAGATATCTCAAACCAACTAATCTTTTCATT
AATACTGAAGACGTGAGGCTGAAGATAGGGGACTTTTGTCTTGCACAAATCAGGGATCCTCATTATTCCCATAAGGATCA
TCTTTCTGAAGGACTGGTAACTAAATGGTACAGATCTCCACATCTTTTACATTCTCCTAGTAGTTATAGTAAAGCCATTG
ACATGTGGGCTGCAGGCCACATCTTTGCTGAAAGGCTGACTGGTAAAACCCTTTTTGCAGGTGCACGTGAACTCAAACAG
ATGGAGCTGATTTTAGAATCTAGTCCTGTTATACATGAGGAAGATCGTCAGGAGCTTCTCAGGGAAATTCCAGTTTACGT
TAGAAATGAAATGACTGAACCACAGAAAGCTTTAACTCAGCTGCTTCAGGGAATTAGTTGAGAAGCACTGGATCTCCTGG
AACAAATTTTGACATTTATCCCTAGCGATGGGTTAACAGCAGAAGAAGCGCTCTCCCTTCATTACATGAGCATATATTAT
TTTCCAATGGATGAGCCAATTTCAAGTTATCTTTTTCACATTGAAGACGAAGTTTATGATATTTTGCTTATGGATGAAAC
TCACAGTCACATTTATAACTGGGAAAGGTATGATTGTTAGTTTTCAGTGCATGATTGGCCTATACATAACAACTTTGACA
TTGATGAAGTTCTGCTTGACCCAAGAGCTCTGTCTGATGTCACTGATGAAGAAGAAGTACAAGTTGATCCCCAAAAATAT
TTGGATGGACGTTGGGAAAAGTAT

Alignment

ORF - retro_pabe_1853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.81 %
• Parental protein coverage: 60.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVFS-AVDNDCDKRVAIKKIVLTDPQSVKHALREIKII
          .AEK.ESLMNIHGFDLG..YM.LKPL..GGN.L....AVDNDCDKR..IKKI.LTDPQSVK.AL.EIKII
Retrocopy LAEKAESLMNIHGFDLGTGYMNLKPLDSGGNSLXXX>AVDNDCDKRESIKKILLTDPQSVKNALHEIKII

Parental  RRLD-HDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLR
          RR.D.H..IVKVFEI...SGSQLT..V.SLT.LNS.YI.Q.YMETDLAN.LE.GPLLE.HARLFMYQLLR
Retrocopy RRFD<HRDIVKVFEIPSTSGSQLTNNVNSLTKLNSIYIFQNYMETDLANMLEEGPLLEKHARLFMYQLLR

Parental  GLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNN
          .LKYIHSANVL.R.LKP.NLFINTED..LKIGDF.LA.I.DPHYSHK.HLSEGLVTKWYRSP.LL.SP..
Retrocopy WLKYIHSANVLPRYLKPTNLFINTEDVRLKIGDFCLAQIRDPHYSHKDHLSEGLVTKWYRSPHLLHSPSS

Parental  YTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHRPL
          Y.KAIDMWAAG.IFAE.LTGKTLFAGA.EL.QM.LILES.PV.HEEDRQELL..IPVY.RN.MTEP...L
Retrocopy YSKAIDMWAAGHIFAERLTGKTLFAGARELKQMELILESSPVIHEEDRQELLREIPVYVRNEMTEPQKAL

Parental  TQLLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETH
          TQLL.GIS.EALD.LEQILTF.P.D.LTAEEALS..YMSIY.FPMDEPISS..FHIEDEV.DILLMDETH
Retrocopy TQLLQGIS*EALDLLEQILTFIPSDGLTAEEALSLHYMSIYYFPMDEPISSYLFHIEDEVYDILLMDETH

Parental  SHIYNWERYHDCQFSEHDWPVHNNFDIDEVQLDPRALSDVTDEEEVQVDPRKYLDGDREKY
          SHIYNWERY.DC.FS.HDWP.HNNFDIDEV.LDPRALSDVTDEEEVQVDP.KYLDG..EKY
Retrocopy SHIYNWERY-DC*FSVHDWPIHNNFDIDEVLLDPRALSDVTDEEEVQVDPQKYLDGRWEKY

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	41.30 RPM
SRP007412_cerebellum	0.00 RPM	82.32 RPM
SRP007412_heart	0.00 RPM	10.69 RPM
SRP007412_kidney	0.00 RPM	21.28 RPM
SRP007412_liver	0.00 RPM	40.85 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1853 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1853 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2519
Pan troglodytes	retro_ptro_1464
Gorilla gorilla	retro_ggor_1571

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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,
Pongo abelii	ENSPPYG00000007239	1 retrocopy	retro_pabe_1440,
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,