RetrogeneDB ID: retro_ptro_2743

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:44568095..44569734(-)
• 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_2743
ATGGCAGAGAAATTTGAAAGTCTCATGAACATTCATGTTTTTGATCTGGGTTCCAGGTATATGGTCTTAAAACCGTTGGG
TTGTGGAGGCAATGGCTTGGTTTTTTTCTGCTATAGACAATGACTGTGACAAAAGAGTGGCCATCAAGAAAATGGTCCTT
ACCAATTCCCAGAATGTCAAACATGCTGTACGTAAAATCAAAATTATTAGAAGACTTGACCATGACAACACTGTGAAAGT
GTTTGAAATTCTTGGTCCCAGGGGAAACAGACGATGTGGGCTCTCTTACAGAGCTGAACAGTGTTTACATTGCTCAGGAG
TACATGGAGACAGACTTAGCTAATGTGCTGGAGCAGGGCACTTTACTGGAAGAGCATGCCAGGCTTTTCATGTATCAGCT
GCTACGGGGGGTCAAGAATATTCACTCTGCAAATGTACTGCACAGAGATCTCAAACCAGTGAATCTTTTCATTAATACTG
AAGACTTGGTGCTGAAGATATGTGACTTTGGTCTTGCACGGATTACAAATACTGATTATTCCCATAAGGGTCATCTTTCT
GAAGGATTGGTTACTAAATGGTACAGATGTCCACGTCTTTTACTTTCTCCTAACAGTTATACTAAAGCCATTGACATGTG
GGCTGCAGGCTGCATCTTTGCTGAAATGCTGACTGGTAAAATCCTTTTTGCAGGTGCACATGAACTTGAACAGATGCAAC
TGATTTTATAATCGATTCCTGTTGCACATTGAAGATCATCAGGAGCTTCTCAGTGTAATTCCAGTTTACATTAGAAATGA
CATGACTGAGCCACACAAACCTTTAACTCAGGTGTTTCCAGGAATTAGTCGAGAAGCACTGGATTTCCTGGAACAAATTT
TTACATTTAGCTCCATGGATTGGTTAACAGCAGAAGAAGCTCTCTCCCATTCTTACATGAGCATATACTCTTTTCCAACG
GATGAGCCAATTTCAAGCCATCCTTTTCGTATTGAAGATGAAGTTGATAATATTTTGCTTATGGATGAAACTCACAGTTA
CATTTATAACTGGGAAAGGTACCATGATAGTCAGCTTTCAGATTGTGATTGGCCTATACATAACAACTTTGATATTGATG
AAGTTCAGCCTGATCCAAGAGCTCTGTCTGATGTCACTGATGAAAAAGAAGTACAAGTTGATCCCCGAAAATATTTGGAT
GGAGATTGGGAAAAGTATCTGGAGGACCTTACTTTTGATACCAATTATTCTACTGAGCCTTGTTGGCAGTACCAAGGATC
ATCATGAAAACAAATATTGTGATCTGGAGTGTAGCCATACTTGTAACTACAAAACGAGGTCATCATCATATTTAGATAAC
TTAGTTTGGAGAGGGAGTGAAGTTAACCATTACTATGAACTCAGGCTTGTTATAGATCTTTCCAATTGGAAAGAACAAAG
CAAAGAAAAATCTGATAAGAAAGGCAAATCAAAATGTGAAAGGTATGGATTGGTTAAAGCCCAGATAGCACTAGAGGAAG
CATTGTAGCAACTGGCTGGAAAAGAAAGAGAAAAGAATCAGGGGTTTGACTTTGATTCTTTTATTGCAGGAACTGTTCAT
CTTAGTTCCCAATATGAGCCTACTGATGTTGTTGATAAA

Alignment

ORF - retro_ptro_2743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.81 %
• Parental protein coverage: 76.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVF-SAVDNDCDKRVAIKKIVLTDPQSVKHALREI-KI
          MAEKFESLMNIH.FDLGSRYM.LKPLGCGGNGLVF.SA.DNDCDKRVAIKK.VLT..Q.VKHA.R.I.K.
Retrocopy MAEKFESLMNIHVFDLGSRYMVLKPLGCGGNGLVF>SAIDNDCDKRVAIKKMVLTNSQNVKHAVRKI>KL

Parental  IRRLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLR
          ...L......K....L.P.....TDDVGSLTELNSVYI.QEYMETDLANVLEQG.LLEEHARLFMYQLLR
Retrocopy LEDLTMTTL*KCLKFLVPGE---TDDVGSLTELNSVYIAQEYMETDLANVLEQGTLLEEHARLFMYQLLR

Parental  GLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNN
          G.K.IHSANVLHRDLKP.NLFINTEDLVLKI.DFGLARI....YSHKGHLSEGLVTKWYR.PRLLLSPN.
Retrocopy GVKNIHSANVLHRDLKPVNLFINTEDLVLKICDFGLARITNTDYSHKGHLSEGLVTKWYRCPRLLLSPNS

Parental  YTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVH-EEDRQELLSVIPVYIRNDMTEPHKP
          YTKAIDMWAAGCIFAEMLTGK.LFAGAHELEQMQLIL.SIPV.H.E.....LLSVIPVYIRNDMTEPHKP
Retrocopy YTKAIDMWAAGCIFAEMLTGKILFAGAHELEQMQLIL*SIPVAH>EDHQE-LLSVIPVYIRNDMTEPHKP

Parental  LTQLLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDET
          LTQ..PGISREALDFLEQI.TFS.MD.LTAEEALSH.YMSIYSFP.DEPISSHPF.IEDEVD.ILLMDET
Retrocopy LTQVFPGISREALDFLEQIFTFSSMDWLTAEEALSHSYMSIYSFPTDEPISSHPFRIEDEVDNILLMDET

Parental  HSHIYNWERYHDCQFSEHDWPVHNNFDIDEVQLDPRALSDVTDEEEVQVDPRKYLDGDREKYLEDPAFDT
          HS.IYNWERYHD.Q.S..DWP.HNNFDIDEVQ.DPRALSDVTDE.EVQVDPRKYLDGD.EKYLED..FDT
Retrocopy HSYIYNWERYHDSQLSDCDWPIHNNFDIDEVQPDPRALSDVTDEKEVQVDPRKYLDGDWEKYLEDLTFDT

Parental  NYSTEPCWQY-SDHHENKYCDLECSHTCNYKTRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEK
          NYSTEPCWQY..DHHENKYCDLECSHTCNYKTRSSSYLDNLVWR.SEVNHYYE..L.IDLSNWKEQSKEK
Retrocopy NYSTEPCWQY>KDHHENKYCDLECSHTCNYKTRSSSYLDNLVWRGSEVNHYYELRLVIDLSNWKEQSKEK

Parental  SDKKGKSKCERNGLVKAQIALEEASQQLAGKEREKNQGFDFDSFIAGTIQLSSQHEPTDVVDK
          SDKKGKSKCER.GLVKAQIALEEA..QLAGKEREKNQGFDFDSFIAGT..LSSQ.EPTDVVDK
Retrocopy SDKKGKSKCERYGLVKAQIALEEAL*QLAGKEREKNQGFDFDSFIAGTVHLSSQYEPTDVVDK

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	0.11 RPM	164.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2743 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2743 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2743 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3322

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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,