RetrogeneDB ID: retro_pabe_3322

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:48298171..48299786(-)
• 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_3322
ATGGCAGAGAAATTTGAAAGTCTCATGAACATTCATGTTTTTGATGTGGGTTCTAGGTATATGGTCTTAAAACCATTGGG
TTGTGGAGGCAATGGCTTGGTTTTTTTCTGCTGTAGACAATGACTGTGACAAAAGAGTGGCCATCAAGAAAATGGTCCTT
ACCAAACCCCAGAGTGTCAAACATGCTGTACGTAAAATCAAAATTATTAGAAGACTTGACCATGATAACACTGTGAAAGT
GTTTGAAATTCTTGGTCCCAGGGGAAACAGACAATGTGGGCTCTCTTACAGAGCCGAACAGGGTTTACATTGCTCAGGAG
TATGTGGAGACAGACTTAGCTAATGTGCTGGAGCAGGGCACTTTACTGGAAGAGCATGCCAGGCTTTTCATGTATCAGCT
GCTACAGGGGCTCAAGTATATTCACTCTGCAAATGTACTGCACAGAGATCTCAAACCAGCGAATCTTTTCATTAACACTG
AAGACTTGGTGCTGAAGATATGTGACTTTGGTCTTGCATGGATCATGAATACTCATTATTCCCGTAAGGGTCATCTTTCT
GAAGGACTGGTTACTAAATGGTACAGATCTCCACGTCTTTTACTTTCTCCTAATGATTATACTAAAGCCATTGACATGTG
GGCTGCAGGCTGCATCTTTGCTGAAATGCTGACTGGTAAAATCCGTTTTGCAGGTGCACATGAACTTGAACAGATGCAGC
TGATTTTATGATCGATTCCTGTTGCACATTGAAGATCATCAGGAGCTTCTCAGTGTAATTCCAGTTTACATTAGAAATGA
CATGACTGAGCCACACAAACCTTTAACTCAGGTGTTTCCAGGAATTAGTTGAGAAGCACTGGATTTCCTGGAACAAATTT
TTACATTTAGCTCCATGGACTGGTTAACAGCAGAAGAAGCTCTCTCCCATTCTTACATGAGCATATACTCTTTTCCAATG
GATGAGCCAATTTCAAGCCATCCTTTTCATATTGAAGATGAAGTTGATAATATTTTGCTTATGGATAAAACTCACAGTTA
CATTTATAACTGGGAAAGGTACCATGATTGTCAGTTTTCAGAGTATGATTGGCCTATACATAACAACTTTGATATTGATG
AAGTTCAGCTTGATCCAAGAGCTCTGTCTGATGTCACTGATGAAAAAGAAGTACAAACTGATCCCCAAAAATATTTGGAT
GGAGATCGGGAAAAGTATCTGGAGGACCTTACTTTTGATACCAATTATTCTACTGAGCCTTGGCAGTACCAAGGATCATC
ATGAAAACAAATATTGTGATCTGGAGTGTAGCCATACTTGTAACTACAAAACGACGTCATCATCATATTTAGATAACTTA
GTTTGGAGAGAGAGTGAAGTTAACCATTACTATGAACCCAGGCTTATTATAGATCTTTCCAATTGGAAAGAACAAAGCAA
AGAAAAATCTGATAAGAAAGGCACATCAAAATGTGAAAGGTATGGATTGGTTAAAGCCTAGATAGCACTAGAGGAAGCAT
CATAGCAACTGGCTGGAAAAGAAAGAGAAAAGAATCAGGGGTTTGACTTTGATTCTTTTATTGCAGGAACTGTTCAACTT
AGTTTCCAACATGAG

Alignment

ORF - retro_pabe_3322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.98 %
• Parental protein coverage: 80.53 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVF-SAVDNDCDKRVAIKKIVLTDPQSVKHALREI-KI
          MAEKFESLMNIH.FD.GSRYM.LKPLGCGGNGLVF.SAVDNDCDKRVAIKK.VLT.PQSVKHA.R.I.K.
Retrocopy MAEKFESLMNIHVFDVGSRYMVLKPLGCGGNGLVF>SAVDNDCDKRVAIKKMVLTKPQSVKHAVRKI>KL

Parental  IRRLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLR
          ...L......K....L.P.....TD.VGSLTE.N.VYI.QEY.ETDLANVLEQG.LLEEHARLFMYQLL.
Retrocopy LEDLTMITL*KCLKFLVPGE---TDNVGSLTEPNRVYIAQEYVETDLANVLEQGTLLEEHARLFMYQLLQ

Parental  GLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNN
          GLKYIHSANVLHRDLKPANLFINTEDLVLKI.DFGLA.IM..HYS.KGHLSEGLVTKWYRSPRLLLSPN.
Retrocopy GLKYIHSANVLHRDLKPANLFINTEDLVLKICDFGLAWIMNTHYSRKGHLSEGLVTKWYRSPRLLLSPND

Parental  YTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVH-EEDRQELLSVIPVYIRNDMTEPHRP
          YTKAIDMWAAGCIFAEMLTGK..FAGAHELEQMQLIL.SIPV.H.E.....LLSVIPVYIRNDMTEPH.P
Retrocopy YTKAIDMWAAGCIFAEMLTGKIRFAGAHELEQMQLIL*SIPVAH>EDHQE-LLSVIPVYIRNDMTEPHKP

Parental  LTQLLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDET
          LTQ..PGIS.EALDFLEQI.TFS.MD.LTAEEALSH.YMSIYSFPMDEPISSHPFHIEDEVD.ILLMD.T
Retrocopy LTQVFPGIS*EALDFLEQIFTFSSMDWLTAEEALSHSYMSIYSFPMDEPISSHPFHIEDEVDNILLMDKT

Parental  HSHIYNWERYHDCQFSEHDWPVHNNFDIDEVQLDPRALSDVTDEEEVQVDPRKYLDGDREKYLEDPAFDT
          HS.IYNWERYHDCQFSE.DWP.HNNFDIDEVQLDPRALSDVTDE.EVQ.DP.KYLDGDREKYLED..FDT
Retrocopy HSYIYNWERYHDCQFSEYDWPIHNNFDIDEVQLDPRALSDVTDEKEVQTDPQKYLDGDREKYLEDLTFDT

Parental  NYSTEPCWQY-SDHHENKYCDLECGHTCNYKTRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEK
          NYSTEP.WQY..DHHENKYCDLEC.HTCNYKT.SSSYLDNLVWRESEVNHYYEP.LIIDLSNWKEQSKEK
Retrocopy NYSTEP-WQY>KDHHENKYCDLECSHTCNYKTTSSSYLDNLVWRESEVNHYYEPRLIIDLSNWKEQSKEK

Parental  SDKKGKSKCERNGLVKAQIALEEASQQLAGKEREKNQGFDFDSFIAGTIQLSSQHE
          SDKKG.SKCER.GLVKA.IALEEAS.QLAGKEREKNQGFDFDSFIAGT.QLS.QHE
Retrocopy SDKKGTSKCERYGLVKA*IALEEAS*QLAGKEREKNQGFDFDSFIAGTVQLSFQHE

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_3322 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3322 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2743

---

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,