RetrogeneDB ID: retro_pabe_3775

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:70953102..70954294(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP2K4
• Ensembl ID: ENSPPYG00000007993
• Aliases: None
• Description: mitogen-activated protein kinase kinase 4 [Source:HGNC Symbol;Acc:6844]

Sequence

>retro_pabe_3775
GCAGCTCCGAGCCTGAGCGGCGGCTGCGGCTCCGGGGCAGCAAGGCAGTGGCACCCCGGGCATGTAGGATCCCTGGAGCC
AGGCCACCCAGCCATCAGCAGCATGCAGGGTAAACGCAAAGCACTGAAGTTGAATTTTGCAAATCCACCTTTCAAATCTA
CAGCAAGGTTTACTCTGAATCCCAATCCTACAGGAGTTCAAAACCCACAGATAGAGAGACTGAGATCACATAGCATTAAG
TCATCAGGAAAACTGAAGATCTCCCCTTAACAACACTGGGATTTCACTGCAGAGGACTTGAAAGACCTTGGAGAAATTGG
ATGAGGAGCTTATGGTTCTGTCAACAAAATGGTTCACAAACCAAGTGGGCAAATAATGGCAGTTAAAAGAATTCGGTCAA
CAGTGAATGAAAAAGAACAAAAACAACCTCTTACGGATTTGGATGAAGTAATGTGGAGTAGTGATTGCCCTTACATTGTT
CAGTTTTATGATGCACTCTTCAGAGAGGGTGACTGTTGGACCTGTATGGAACTCATGTCTATCTCGTTTGATAAGTTTTA
CAAATATGTGTATAGTGTATTAGATGATGTTATTCCAGAAGAAATTGTAGGCAAAATCACTTTAGCAGCTGTGAAAGCAC
TAAATCACTTAAAAGAAAATTTGAAAATTATTCACAGAGACATCAAACCTTCCAAAATTCTTCTGGACAGAAGTGAAAAT
ATTAAACTCTATGACTTTGGCATCAGTGGACAGCTTGTGGACTCTATTGCCAAGACAAAAGATGCTGGCTGTAGGCCATA
CATGGCACCCGAAAGAATAGACCCAAGTGCATCATGACAAGCATATGATGTCCGCTCTGATGTCTGGAGTTTGGGGATCA
CATTGTGTGAGTTGGCCACGGGCCAATTTCCTTATCCAAAGTGGAATAGTATATTTGATCAACTAACACAAGTCGTGAAA
GGAGATCCTCCGCAGCTGAGTAATTCTGAGGAAAGGGAATTCTCCCCAAGTTTCATCAACTTTGTCAACTTGTGCCTTAC
GAAGGATGAATCCAGAAGACCAAAGTATGAAGAGCTTCTGAAACATCTTTTTATTTTGATGTATGAAGAACGTACCGTTG
AGGTTGCATGCTATGTTTGTAAAATCCTGGATCAAATGCCAGCTACTCCCAGCTTTTCCCATGTATGTCGAT

Alignment

ORF - retro_pabe_3775 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.72 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAPSPSGGGGSGGGSGSGTPGPVGSPAPGHPAVSSMQGKRKALKLNFANPPFKSTARFTLNPNPTGVQNP
          AAPS.SG.G...G......PG.VGS..PGHPA.SSMQGKRKALKLNFANPPFKSTARFTLNPNPTGVQNP
Retrocopy AAPSLSG-GCGSGAARQWHPGHVGSLEPGHPAISSMQGKRKALKLNFANPPFKSTARFTLNPNPTGVQNP

Parental  HIERLRTHSIESSGKLKISPEQHWDFTAEDLKDLGEIGRGAYGSVNKMVHKPSGQIMAVKRIRSTVDEKE
          .IERLR.HSI.SSGKLKISP.QHWDFTAEDLKDLGEIG.GAYGSVNKMVHKPSGQIMAVKRIRSTV.EKE
Retrocopy QIERLRSHSIKSSGKLKISP*QHWDFTAEDLKDLGEIG*GAYGSVNKMVHKPSGQIMAVKRIRSTVNEKE

Parental  QKQLLMDLDVVMRSSDCPYIVQFYGALFREGDCWICMELMSTSFDKFYKYVYSVLDDVIPEEILGKITLA
          QKQ.L.DLD.VM.SSDCPYIVQFY.ALFREGDCW.CMELMS.SFDKFYKYVYSVLDDVIPEEI.GKITLA
Retrocopy QKQPLTDLDEVMWSSDCPYIVQFYDALFREGDCWTCMELMSISFDKFYKYVYSVLDDVIPEEIVGKITLA

Parental  TVKALNHLKENLKIIHRDIKPSNILLDRSGNIKLCDFGISGQLVDSIAKTRDAGCRPYMAPERIDPSASR
          .VKALNHLKENLKIIHRDIKPS.ILLDRS.NIKL.DFGISGQLVDSIAKT.DAGCRPYMAPERIDPSAS.
Retrocopy AVKALNHLKENLKIIHRDIKPSKILLDRSENIKLYDFGISGQLVDSIAKTKDAGCRPYMAPERIDPSAS*

Parental  QGYDVRSDVWSLGITLYELATGRFPYPKWNSVFDQLTQVVKGDPPQLSNSEEREFSPSFINFVNLCLTKD
          Q.YDVRSDVWSLGITL.ELATG.FPYPKWNS.FDQLTQVVKGDPPQLSNSEEREFSPSFINFVNLCLTKD
Retrocopy QAYDVRSDVWSLGITLCELATGQFPYPKWNSIFDQLTQVVKGDPPQLSNSEEREFSPSFINFVNLCLTKD

Parental  ESKRPKYKELLKHPFILMYEERAVEVACYVCKILDQMPATPS-SPMYVD
          ES.RPKY.ELLKH.FILMYEER.VEVACYVCKILDQMPATPS..PMYVD
Retrocopy ESRRPKYEELLKHLFILMYEERTVEVACYVCKILDQMPATPS>FPMYVD

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	0.06 RPM	80.01 RPM
SRP007412_cerebellum	0.00 RPM	69.43 RPM
SRP007412_heart	0.00 RPM	11.62 RPM
SRP007412_kidney	0.00 RPM	14.58 RPM
SRP007412_liver	0.00 RPM	15.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3775 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3775 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3775 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4858

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000065559	1 retrocopy	retro_hsap_4858,
Monodelphis domestica	ENSMODG00000008266	2 retrocopies	retro_mdom_1281, retro_mdom_957,
Mustela putorius furo	ENSMPUG00000003664	1 retrocopy	retro_mputfur_1419,
Pongo abelii	ENSPPYG00000006576	2 retrocopies	retro_pabe_3092, retro_pabe_3249,
Pongo abelii	ENSPPYG00000007993	1 retrocopy	retro_pabe_3775 ,
Tarsius syrichta	ENSTSYG00000011568	1 retrocopy	retro_tsyr_667,