RetrogeneDB ID: retro_ptro_3045

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392075.1:3114703..3115888(-)
• Located in intron of: ENSPTRG00000005823

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_3045
AAAACCCTTTTTGCAGGTGCACATGAACTTGAACAGATGCAGCTGACTTTCGAATCTATTCCTGTTGCACATGAGGAAGA
TCGTCAGGAGCTTCTCAGCGTAATTCCAGTTTACATTAGAAATCACATGACTGAGCCACAGAAACCTTTAACTCAGCTAC
TTCCAGGAATTAGTCGAGAAGCACTGAATTTCCTGGAACAAATTTTGACATTTAGCCCCATGGATCAGTTAATAGCAGAA
GAAGCACTCTCCCATCCTTACATGAGCATATATTCTTTTCCAATGGATAAGCCAATTTCAAGCCATCCTTTTCATATTGA
AGATGAAGCTCATAATATTTTGCTTATGGATGAAACTCACAGTCACATTTATAACTGGGAAAGGTACTATGACTGTCAGT
TTTCAGAGCATGATTGGCCTATACTTAACAACTTTGATATTGATGAAGTTCAGCTTGATCCAAGAGCTCTGTCTGATGTC
ACTGATGAAGAAGTACAAGTCGATCCCCGAAATTATTTGGATGGAGATCGGGAAAGGTATCTGGGGGATCCTGCTTTTGA
TACCAATTACTCTGCTGAGCCTTGTTGGCAGTACCCAGATCATCATGAAAACAAATATTGTGATCTGGAGTGTAGCCATA
CTTGTAATTACAAAACGAGGTCATGATCATATTTAGATAACTTAGTTTGGAGAGAGAATGAAGTTAACCGTTACTATGAA
CCCAAGCTTATTACAGATCTTTCCAATTGGAAAGAACAAAGCAAAGAAAAATCTGATAAGAAAAGCAAATCAAAATGTGA
AAGGAATGGATTGGTTAAAGCCCAGATAGTGCTAGAGGAAGCATCACGGCAACTGGCTGGAAAAGAAAGGGAAAAGAATC
AGGGATTTGATTTTCATTCCTTTATTGCAGGAACTATTCAATTTAGTTTCCAACATGAGCCTACTAATGTTGTTGATAAA
TTAAATGACTTGAATAGCTCAGTGTCCCAACTAGAATTGAAAAGTTTGATATCAAAGTCAGTAAGCCAAGAAAAACAGGA
AAAAGGAATGGCAAATCTGGCTCAATTAGAAACTTTGTACCCATCTTCTTGGGACAGCCAGTTTGTGAGTGATGGGGAGA
ACTGTTTTCCCATAAATCAGTTTTGTGAAGTAAGAAAGGATGAACAAGTTAAGAAGGAAAACACA

Alignment

ORF - retro_ptro_3045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.4 %
• Parental protein coverage: 54.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREALDFLEQILT
          KTLFAGAHELEQMQL..ESIPV.HEEDRQELLSVIPVYIRN.MTEP.KPLTQLLPGISREAL.FLEQILT
Retrocopy KTLFAGAHELEQMQLTFESIPVAHEEDRQELLSVIPVYIRNHMTEPQKPLTQLLPGISREALNFLEQILT

Parental  FSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSHIYNWERYHDCQFSEHDWP
          FSPMD.L.AEEALSHPYMSIYSFPMD.PISSHPFHIEDE...ILLMDETHSHIYNWERY.DCQFSEHDWP
Retrocopy FSPMDQLIAEEALSHPYMSIYSFPMDKPISSHPFHIEDEAHNILLMDETHSHIYNWERYYDCQFSEHDWP

Parental  VHNNFDIDEVQLDPRALSDVTDEEEVQVDPRKYLDGDREKYLEDPAFDTNYSTEPCWQYSDHHENKYCDL
          ..NNFDIDEVQLDPRALSDVTDEE.VQVDPR.YLDGDRE.YL.DPAFDTNYS.EPCWQY.DHHENKYCDL
Retrocopy ILNNFDIDEVQLDPRALSDVTDEE-VQVDPRNYLDGDRERYLGDPAFDTNYSAEPCWQYPDHHENKYCDL

Parental  ECSHTCNYKTRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDKKGKSKCERNGLVKAQIALE
          ECSHTCNYKTRS.SYLDNLVWRE.EVN.YYEPKLI.DLSNWKEQSKEKSDKK.KSKCERNGLVKAQI.LE
Retrocopy ECSHTCNYKTRS*SYLDNLVWRENEVNRYYEPKLITDLSNWKEQSKEKSDKKSKSKCERNGLVKAQIVLE

Parental  EASQQLAGKEREKNQGFDFDSFIAGTIQLSSQHEPTDVVDKLNDLNSSVSQLELKSLISKSVSQEKQEKG
          EAS.QLAGKEREKNQGFDF.SFIAGTIQ.S.QHEPT.VVDKLNDLNSSVSQLELKSLISKSVSQEKQEKG
Retrocopy EASRQLAGKEREKNQGFDFHSFIAGTIQFSFQHEPTNVVDKLNDLNSSVSQLELKSLISKSVSQEKQEKG

Parental  MANLAQLEALYQSSWDSQFVSGGEDCFFINQFCEVRKDEQVEKENT
          MANLAQLE.LY.SSWDSQFVS.GE.CF.INQFCEVRKDEQV.KENT
Retrocopy MANLAQLETLYPSSWDSQFVSDGENCFPINQFCEVRKDEQVKKENT

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	0.02 RPM	39.31 RPM
SRP007412_cerebellum	0.04 RPM	72.23 RPM
SRP007412_heart	0.00 RPM	14.86 RPM
SRP007412_kidney	0.00 RPM	25.99 RPM
SRP007412_liver	0.03 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_3045 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3045 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1257

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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,