RetrogeneDB ID: retro_pabe_457

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:151281398..151282576(-)
• Located in intron of: ENSPPYG00000001221

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSRP1
• Ensembl ID: ENSPPYG00000008130
• Aliases: NSRP1, CCDC55
• Description: nuclear speckle splicing regulatory protein 1 [Source:HGNC Symbol;Acc:25305]

Sequence

>retro_pabe_457
ATGGTGATTCTGGGCAGGCAGTATGGGCTTATTTTGCCAAAGAAAACACAGCAGTTGCATCCTGTTTTGCAAAAAACATC
AGTGTTTGGGAATGATTCTGATGATGATGATGAGACCTCCATGAGTGAAAGCCTTTAGAAGGAAGCTACTAAGAAGCAGG
CCATGAAACAGACCAAACTGGAATCCAGAAGGCCCTTGCAGAAGATGCTACTGTGTATGAATATGACAGTATTTATGATG
AAATGCAGAAAAAAATAAGAGGAAAACAATCCCAAATTGCTTTTGGGGAAAGACCGAAAGCCCAAGTATATTCACAACTT
GCTAAAAGCAGTTGAGATCAGAAAAAAGGAACAGGAAAAAAGAATGGAAAAGAAAATACAGAGAGAACGAGAAATGGAAA
AGGGAGAGTTTGATGATAAAGAGACATTGTGACATCTGCATATAAGAAAAAACTGCAAGGGACAGCTGAAGAAGAAAGAA
AAAAGAGGGCTGCTGCGCTGGAAGCATGTTTGGATGTAACCAAGCAGAAAGATCTCGGTGGATTTTATAGGCACTTATTA
AATCAAGCAGTTGGTGAAGAGGAAGTACCTAAATGCAGCTTTCGTGAAGCCAGATCTGGTATAAAGGAAGAGAAATCAAG
GGGCTACTCTGATGAAGTAAGTTCAAAAAACAGAATACAAGAGAAATGCATTCTTCAAACTGATCTGAAAGTAGAGGAAA
ACCCAGATGCAGACAGTGACTTTGATGCTAAGAGCAGCAAGGATGATGAAATAGAAGAAACTAGAGTGAACTGCAGAAGG
GAAAAGGTCGTAGAGATCCCTGAGAATGACCCCCAAGCACCACAGGAATCAAAACCACTCTCAGTCACCTAGTGAAGAAA
TAGGGCACAGTGCCAGACACCACACGAAAGGATCACGAACGTCGAGAGGACATGAGAAAAGGGAAGATCAGCACCAACAG
AAGCAATCCAGAGATGAGGAGAACCATTACACTGACCGTGATTACCGGAAAGAAAGGGATTCTCATAGGCACAGGAGGCC
AGTCACAGAGATTCCCATTGGAAGAGGCATGAACAGGAAGATAAACCAAGGGCGAGGGACCAAAGAGAAAGAAGTGACAG
AGTGTGGAAAAGGGAGAAAGACGGGGAGAAATATTCCCAAAGAGAACAAGAAAGAGAG

Alignment

ORF - retro_pabe_457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.25 %
• Parental protein coverage: 70.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAIPGRQYGLILPKKTQQLHPVLQKPSVFGNDSDDDDETSVSESLQREAAKKQAMKQTKLE-IQKALAED
          M.I.GRQYGLILPKKTQQLHPVLQK.SVFGNDSDDDDETS.SESL..EA.KKQAMKQTKLE.IQKALAED
Retrocopy MVILGRQYGLILPKKTQQLHPVLQKTSVFGNDSDDDDETSMSESL*KEATKKQAMKQTKLE<IQKALAED

Parental  ATVYEYDSIYEEMQKKK-EENNPKLLLGKDRKPKYIHNLLKAVEIRKKEQEKRMEKKIQREREMEKGEFD
          ATVYEYDSIY.EMQKK..EENNPKLLLGKDRKPKYIHNLLKAVEI.............QREREMEKGEFD
Retrocopy ATVYEYDSIYDEMQKKI>EENNPKLLLGKDRKPKYIHNLLKAVEIXXXXXXXXXXXXXQREREMEKGEFD

Parental  DKEA-FVTSAYKKKLQERAEEEEREKRAAALEACLDVTKQKDLSGFYRHLLNQAVGEEEVPKCSFREARS
          DKE...VTSAYKKKLQ..A.EEER.KRAAALEACLDVTKQKDL.GFYRHLLNQAVGEEEVPKCSFREARS
Retrocopy DKET<IVTSAYKKKLQGTA-EEERKKRAAALEACLDVTKQKDLGGFYRHLLNQAVGEEEVPKCSFREARS

Parental  GIKEEKSKGYSNEVSSKNRIPQEKCVLQTDVKVEENPDADSDFDAKSSEDDEIEETRVNCRREKVIETPE
          GIKEEKS.GYS.EVSSKNRI.QEKC.LQTD.KVEENPDADSDFDAKSS.DDEIEETRVNCRREKV.E.PE
Retrocopy GIKEEKSRGYSDEVSSKNRI-QEKCILQTDLKVEENPDADSDFDAKSSKDDEIEETRVNCRREKVVEIPE

Parental  ND-SKHHRNQNHSRSPSEERGHSTRHHMKGSRTSRGHEKREDQHQQKQSRDQENRYTDRDYRKERDSHRH
          ND..KHHRNQNHS.SPSEE.GHS.RHH.KGSRTSRGHEKREDQHQQKQSRD.EN.YTDRDYRKERDSHRH
Retrocopy ND>PKHHRNQNHSQSPSEEIGHSARHHTKGSRTSRGHEKREDQHQQKQSRDEENHYTDRDYRKERDSHRH

Parental  R-EASHRDSHWKRHEQEDKPRARDQRERSDRVWKREKDREKYSQREQERD
          R.EASHRDSHWKRHEQEDKPRARDQRERSDRVWKREKD.EKYSQREQER.
Retrocopy R<EASHRDSHWKRHEQEDKPRARDQRERSDRVWKREKDGEKYSQREQERE

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	0.28 RPM	20.02 RPM
SRP007412_cerebellum	0.61 RPM	29.79 RPM
SRP007412_heart	0.09 RPM	23.93 RPM
SRP007412_kidney	0.17 RPM	31.66 RPM
SRP007412_liver	0.00 RPM	14.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_457 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_457 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_457 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_162

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009868	1 retrocopy	retro_mdom_391,
Pongo abelii	ENSPPYG00000008130	1 retrocopy	retro_pabe_457 ,
Pan troglodytes	ENSPTRG00000008957	1 retrocopy	retro_ptro_162,
Sarcophilus harrisii	ENSSHAG00000003513	1 retrocopy	retro_shar_342,