RetrogeneDB ID: retro_pabe_2700

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:157141605..157143455(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000015980
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KIF4A
• Ensembl ID: ENSPPYG00000020438
• Aliases: None
• Description: kinesin family member 4A [Source:HGNC Symbol;Acc:13339]

Sequence

>retro_pabe_2700
GAGCAGTCCAAACTTCTGAAACTAAAGGAATCCACAGAGCATACTGTCTCCAAGCTGAACCAAGAGATATGGATGATGAA
AAACCAGCGGGTACAGTTAATGCGTCAAATGAAAGAGGATGCTGAGAAGTTTAGACAGTGGAAGCAGAAAAAAGATAAAG
AAGTAATACAGTTAAAAGAACGAGACCGTAAGAGGCAATATGAGCTGCTCAAACTTGAAAGAAACTTCCAGAAACAATCC
AGTGTGCTCAGACGTAAAACGGAAGAGGCAGCAGCTGCCAACAAGCGTCTCAAGGATGCTCTCCAGAAACAACGAGAGGT
CACAGATAAGCGGAAAGAGACTCAGAGCCGTGGAATGGAAGCATTGCAGCTCGAGTGAGGAATTGGCTTGGAAATGAAAT
TGAGGTTCTGGTCAGTACTGAGGAAGCCAAACGCCATCTGAATGACCTCCTTGAAGACAGAAAGATCCTGGCTCAGGATG
TGGTTCAACTCAAAGAAAAAAAGGAATCTCGGGAGAATCCACCTCCTAAACTCTGGAAGTGTACATTCTCCCTTACTGAG
GTGCATGGTCAAGTTTTGGAGTCAGAAGATTGTATTACAAAACAGATTGAAAGCCTAGAGACTGAAATGGAACTCAGGAG
TGCTCAGATTGCTGACCTACAGCAGAAGCTCCTGGATGCAGAAAGTGAAGACAGGTCAAAACAATGCTGGGAGAATATTG
CCACCATTCTGGAAGCCAAGTGTGCCCTGAAATATTTGATTGGAGAGCTGGTCTCCTCCAAAATACATGTCACCAAACTT
GAAAACAGCCTGAGACAGAGCAAGGCCAGCTGTGCTGACATGCAGAAGATGCTATTTGAGGAACAAAATCATTTTTCTGA
GATAGAGACAGATTTACAAGCTGAGCTGGTCAGAATGGAGCAACAGCACCAAGAGAAGGTGCTGTACCTTGTCAGCCAGC
TGCAGCAAAGCCAAATGGCAGAGAAGCAGTTACAGAAATCAGCCAGTGAAAAGGAACAGCAGCTGGTGAGCACACTGCAG
TATCAGGATGAAGAACTTGAGAAGATGCGAGAAGTGTGTGAGCAAAATCAGCAGCTTCTCCAAGAGAATGAAATCATCAA
GCAGAAACTGATCCTCCTCCAGGTAGCCAGCAGACAGAAACATCTTCCTAATGATACCCTTCTATCTCCAGACTCTTCTT
TTGAATATATCCCACCTAAGCCAAAACCTTCTCGTGTTAAAGAAAAGTTTCTGGAGCAAAGCATGGACATCGAGGATCTA
AAATATTGTTCAGAGCATTCTGTGAATGAGCATGAAGATGGTGATGGTGATGGCGACGGTGATGAGGGGGATGATGAGGA
ATGGAAGCCAACAAAATTAGTCAAGGTGTCCAGGAAGAATATCCAAGGGTGTTCCTGCAAGGGCTGGTGTGGGAACAAGC
AGTGTGGGTGCAGGAAGCAAAAGTCAGACTGTGGTGTGGACTGTAGCTGTGACCCCACAAAGTGTCGGAACCGCCAGCAA
GGCAAGGATAGCTTGGGCACTGTTGAACAGACCCAGGATTCCGAAGGCTCCTTCAAACTGGAGGATCCTACCGAGGTGAC
CCCAGGATTGAGCTTCTTTAACCCTGTTTGTGCCACCCCCAATAGCAAGATCCTGAAAGAGATGTGTGACATGGAGCAGG
TGCTGTCAAAGAACACTGCTCCAGCTCCCTCCCCTTTTGACCTCCCAGAGTCGAAACATGGAGCAACAGAATACCAACAA
AATAAGCCTCCAGGGAAGAAAAAGAAACGAGCTCTGGCCAGCAACACCAGCTTCTTCTCTGGCTGCTCCCCTATCGAAGA
AGAGGCCCAC

Alignment

ORF - retro_pabe_2700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.45 %
• Parental protein coverage: 63.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQSKLLKLKESTERTVSKLNQEIRMMKNQRVQLMRQMKEDAEKFRQWKQKKDKEVIQLKERDRKRQYELL
          EQSKLLKLKESTE.TVSKLNQEI.MMKNQRVQLMRQMKEDAEKFRQWKQKKDKEVIQLKERDRKRQYELL
Retrocopy EQSKLLKLKESTEHTVSKLNQEIWMMKNQRVQLMRQMKEDAEKFRQWKQKKDKEVIQLKERDRKRQYELL

Parental  KLERNFQKQSNVLRRKTEEAAAANKRLKDALQKQREVADKRKETQSRGMEGT-AARVKNWLGNEIEVMVS
          KLERNFQKQS.VLRRKTEEAAAANKRLKDALQKQREV.DKRKETQSRGME...AARV.NWLGNEIEV.VS
Retrocopy KLERNFQKQSSVLRRKTEEAAAANKRLKDALQKQREVTDKRKETQSRGMEAL<AARVRNWLGNEIEVLVS

Parental  TEEAKRHLNDLLEDRKILAQDVAQLKEKKESGENPPPKLRRRTFSLTEVRGQVSESEDSITKQIESLETE
          TEEAKRHLNDLLEDRKILAQDV.QLKEKKES.ENPPPKL...TFSLTEV.GQV.ESED.ITKQIESLETE
Retrocopy TEEAKRHLNDLLEDRKILAQDVVQLKEKKESRENPPPKLWKCTFSLTEVHGQVLESEDCITKQIESLETE

Parental  MEFRSAQIADLQQKLLDAESEDRPKQRWENIATILEAKCALKYLIGELVSSKIQVSKLESSLKQSKTSCA
          ME.RSAQIADLQQKLLDAESEDR.KQ.WENIATILEAKCALKYLIGELVSSKI.V.KLE.SL.QSK.SCA
Retrocopy MELRSAQIADLQQKLLDAESEDRSKQCWENIATILEAKCALKYLIGELVSSKIHVTKLENSLRQSKASCA

Parental  DMQKMLFEERNHFAEIETELQAELVRMEQQHQEKVLYLLSQLQQSQMAEKQLEESVSEKEQQLLSTLKCQ
          DMQKMLFEE.NHF.EIET.LQAELVRMEQQHQEKVLYL.SQLQQSQMAEKQL..S.SEKEQQL.STL..Q
Retrocopy DMQKMLFEEQNHFSEIETDLQAELVRMEQQHQEKVLYLVSQLQQSQMAEKQLQKSASEKEQQLVSTLQYQ

Parental  DEELEKMREVCEQNQQLLRENEIIKQKLTLLQVASRQKHLPKDTLLSPDSSFEYVPPKPKPSRVKEKFLE
          DEELEKMREVCEQNQQLL.ENEIIKQKL.LLQVASRQKHLP.DTLLSPDSSFEY.PPKPKPSRVKEKFLE
Retrocopy DEELEKMREVCEQNQQLLQENEIIKQKLILLQVASRQKHLPNDTLLSPDSSFEYIPPKPKPSRVKEKFLE

Parental  QSMDIEDLKYCSEHSVNEHEDGDGDGDDDEGDDEEWKPTKLVKVSRKNIQGCSCKGWCGNKQCGCRKQKS
          QSMDIEDLKYCSEHSVNEHE..........GDDEEWKPTKLVKVSRKNIQGCSCKGWCGNKQCGCRKQKS
Retrocopy QSMDIEDLKYCSEHSVNEHEXXXXXXXXXXGDDEEWKPTKLVKVSRKNIQGCSCKGWCGNKQCGCRKQKS

Parental  DCGVDCCCDPTKCRNRQQGKDSLGTVERTQDSEGSFKLEDPTEVTPGLSFFNPVCATPNSKILKEMCDVE
          DCGVDC.CDPTKCRNRQQGKDSLGTVE.TQDSEGSFKLEDPTEVTPGLSFFNPVCATPNSKILKEMCD.E
Retrocopy DCGVDCSCDPTKCRNRQQGKDSLGTVEQTQDSEGSFKLEDPTEVTPGLSFFNPVCATPNSKILKEMCDME

Parental  QVLSKKTPPAPSPFDLPELKHVATEYQENKAPGRKKKRALASNTSFFSGCSPIEEEAH
          QVLSK.T.PAPSPFDLPE.KH.ATEYQ.NK.PG.KKKRALASNTSFFSGCSPIEEEAH
Retrocopy QVLSKNTAPAPSPFDLPESKHGATEYQQNKPPGKKKKRALASNTSFFSGCSPIEEEAH

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	0.39 RPM	0.33 RPM
SRP007412_cerebellum	0.61 RPM	0.00 RPM
SRP007412_heart	0.12 RPM	0.33 RPM
SRP007412_kidney	0.03 RPM	0.17 RPM
SRP007412_liver	0.03 RPM	0.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2700 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2700 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2700 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015566	1 retrocopy	retro_cjac_2142,
Cavia porcellus	ENSCPOG00000000211	1 retrocopy	retro_cpor_681,
Homo sapiens	ENSG00000090889	1 retrocopy	retro_hsap_18,
Gorilla gorilla	ENSGGOG00000006631	1 retrocopy	retro_ggor_2218,
Myotis lucifugus	ENSMLUG00000011048	1 retrocopy	retro_mluc_114,
Mus musculus	ENSMUSG00000034311	1 retrocopy	retro_mmus_268,
Pongo abelii	ENSPPYG00000020438	1 retrocopy	retro_pabe_2700 ,
Rattus norvegicus	ENSRNOG00000038035	1 retrocopy	retro_rnor_2330,