RetrogeneDB ID: retro_pabe_3721

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:8723268..8725026(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOLC1
• Ensembl ID: ENSPPYG00000002595
• Aliases: None
• Description: nucleolar and coiled-body phosphoprotein 1 [Source:RefSeq peptide;Acc:NP_001127603]

Sequence

>retro_pabe_3721
GAAAGCCTCGCCAAAGCATCAGAGAGCAGCACCAGTGAAGCATCCAGTCATGATGAGGAGGACGACAAAAAGAAAAAGTC
TGTCCAGAAGGGAGTTAAGCCCCAAGCCAAGACAGCCAAAGCTCCTCTTAAGAAGGCTAAGAGCTCTGATTCTGATTCTG
ATTCTGACTCAAGCTCTGAGGATGAGGCACCAAAGAAACAGAAACCAAAGACAACATCTGTAGCAGCTAAAGCTCGGGCT
AAAGTCCCAGCCACACCAGGTACTCCAGCTCAAGCAGCACCTAAAGTAGCCAATGGCAAAGCAGCCAGCTGCAACAGCAG
CGGCAGCAGCAGCAGCAGCAGTGGTGACTCAAAGGAAGAGATGGCAGCAGCCATCCCTAAGAAGACTGTATCTTAAAAGC
AAGTTGTGATCAAGGTCCCAGTGAAAGCAGCTGCCACCCCTACCCAAAAATTCCAGCAGTGAGGACTCCTCCGGTGAGGA
GGAAGAGTAGTAGGAAAAAAAAAAAATGAAAAAAAACCCAGGTCCCTAAAGTTCAGTGCCCCCCTCCTGCTCCCCCATCA
AAGAAGTCCTTGGGAACCCAGCCTCCCAAGAAAGCTGTGGAGAAGAAACAGCCTTCCGAAAGCAGTGAAGACAGCAGCAA
CGAGTCTGATTCAAGTTTGGAGGAAGAGGATGAACTCTTGCTAAGTCAGTCATCTCTAAAGCAAATACTAAACAACCTCC
AGCAAAGAAAGCAGCAGAGAGCTCTTCAGAAAGCTCATATTCCAACAGTTCCGAGGATGATGAAGCTCCTTCCAAGCTAG
CCAGTACCAGCAAGAATTCCTCAAATAAGCCAGCTGCCACTACCAAGTCACCTGCAGCGGAGCCAGCTGCAACTCTCAAG
CAACCTGCAAGCAGTGGCCAGAAGCCTCTGACGAGAAAGGCTGACAGCAGCTCCAGTGAGAAAGAGAGCAGTTCCAGTGA
GGAGGAGAAGACAAAGATGACTGTGGCCCCCCTTAAGCCCAAGGTAACTGACAAAGCAGCTCCGTATCTGCCTGCCAAGC
AGGCTCCTGAGGGTGGTAAGGACAGCAGCTCTCATTCAGACAGCTCCAGCAGTGAGGAGGAGGAGGAGGAAGAGAGGACA
TCTAAATCCCCAGTTAAGAAGAAGTTGCAGAAGGCAGCACGAGGGACAGCCCCTTCCAAGCCAGCCTCCACAAAGAAAGG
AAACGTCGAGAGCAGCAGCAATTATTCCTCTGATGACTCCAGTGAGGAAGAGGAAGCGAAGCCCAAGGGCAAGGACTCTC
CAAGACCACAAGTCCCCAAGGCCAATGGCACCTCTGCACTGACTGCCCAGAATGGAAAAGCAGCTAAGAACAGCGAGGAG
GAGGAAGAGGAGGAAGAAGAAAAGAAAAAGGCAGCAGTGGTAGTTTCCAAGCTGGGTTCAGGAAAGAAGTGGAAGCAGCT
GAGACTGCCAAAGAGGCAGAGACTCCTCCAGCCAAGAAAATAAAGCTTCAGACCCCCTAACACATTTCCAAAAAGGAAGA
AAGAAGAAAAAAGGGCATGATCCACATTCTTCAGGGTCAGGGAGAAGGAAATTGAGGTGGCAGACAACTCCATTGATGCC
AGCTGAGGTGCAGCCGGAGACTGGGGGAACGAGCCAATGCGGTTTTGAGGTTCACCAAAGGCAAATCCTTCTGGCATGAG
AAAACCAAGAAGAAGCAGGGCATCTCCTGGGGAGGCTCAATCTCTGTCCAGGTCAATTCTATTAATTTTGACAGTGAG

Alignment

ORF - retro_pabe_3721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.66 %
• Parental protein coverage: 83.29 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KAAAKASESSSSEESSDDEEEDQKKQPVQKGVKPQAKAAKAPPK--KAKSSDSDSDSSSEDEPPKNQKPK
          ...AKASESS.SE.SS.DEE.D.KK..VQKGVKPQAK.AKAP.K..K.........SSSEDE.PK.QKPK
Retrocopy ESLAKASESSTSEASSHDEEDDKKKKSVQKGVKPQAKTAKAPLKKAKSXXXXXXXXSSSEDEAPKKQKPK

Parental  ITPVAVKAQTKA---PPKPARAAPKVANGKAASSSSSSSSSSSSDDSEEEKAAATPKKTVPKKQAMAKAT
          .T.VA.KA..K....P..PA.AAPKVAN.................DS.EE.AAA.PKKTV..KQ...K..
Retrocopy TTSVAAKARAKVPATPGTPAQAAPKVANXXXXXXXXXXXXXXXXGDSKEEMAAAIPKKTVS*KQVVIKVP

Parental  VKAAATPTQK-SSSSEDSSSEEEEEQKKPMKNKPGPYSSVP-PPSAPPPKKSLGTQPPKKAVEKQQPVES
          VKAAATPTQK.SSS...S..EEE..........PGP.SSVP.PP.APP.KKSLGTQPPKKAVEK.QP.ES
Retrocopy VKAAATPTQK>SSSEDSSGEEEE**XXXXXXXXPGP*SSVP>PP-APPSKKSLGTQPPKKAVEKKQPSES

Parental  SEDSSDESDSSSEEEKK-PPTKAVISKATSKPPPAKKAAESSSDSSDSDSSEDDEAPSKPAGTTKNSSNK
          SEDSS.ESDSS.EEE......K.VISKA..K.PPAKKAAESSS.SS.S.SSEDDEAPSK.A.T.KNSSNK
Retrocopy SEDSSNESDSSLEEEDE<TLAKSVISKANTKQPPAKKAAESSSESSYSNSSEDDEAPSKLASTSKNSSNK

Parental  PAVTTKSPAVKPAAAPKQPVGGGQKLPTRKADSSSSEEESSSSEEEKTKKMVATTKPKATAKAAPPLPAK
          PA.TTKSPA..PAA..KQP...GQK..TRKAD...............TK..VA..KPK.T.KAAP.LPAK
Retrocopy PAATTKSPAAEPAATLKQPASSGQKPLTRKADXXXXXXXXXXXXXXXTKMTVAPLKPKVTDKAAPYLPAK

Parental  QAPQGSRDSSSDSDSSSSEEEEEEEKTSKSAVKKKPQKVAGGASPSKPASAKKRKAERSSSSSSDDSSEE
          QAP.G..DSSS.SDSSSS.........SKS.VKKK.QK.A.G..PSKPAS.KK...E.SS..SSDDSSEE
Retrocopy QAPEGGKDSSSHSDSSSSXXXXXXXXXSKSPVKKKLQKAARGTAPSKPASTKKGNVESSSNYSSDDSSEE

Parental  EEEKPKGKGSPRPQAPRANGTSALTAQNGKAAKNSE--EEEEEKKKAA-VVVSKSGSLKKRKQ-NEAAKE
          EE.KPKGK.SPRPQ.P.ANGTSALTAQNGKAAKNSE........KK.A.VVVSK.GS.KK.KQ..E.AKE
Retrocopy EEAKPKGKDSPRPQVPKANGTSALTAQNGKAAKNSEXXXXXXXEKKKAAVVVSKLGSGKKWKQ<AETAKE

Parental  AETPQAKKIKLQT-PNTFPKRKKGEKRASSPFRRVREEEIEVDSRVADNSFDAKRGAAGDW-GERANQVL
          AETP.AKKIKLQT.PNTFPKRKK.EKRA.S.F.RVRE.EIEV....ADNS.DA..GAAGDW.GERAN.VL
Retrocopy AETPPAKKIKLQT>PNTFPKRKKEEKRA*STFFRVREKEIEV----ADNSIDAS*GAAGDW<GERANAVL

Parental  KFTKGKSFRHEKTKKKRGSYRGGSISVQVNSIKFDSE
          .FTKGKSF.HEKTKKK.G...GGSISVQVNSI.FDSE
Retrocopy RFTKGKSFWHEKTKKKQGISWGGSISVQVNSINFDSE

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	88.69 RPM
SRP007412_cerebellum	0.00 RPM	79.04 RPM
SRP007412_heart	0.00 RPM	24.41 RPM
SRP007412_kidney	0.00 RPM	40.97 RPM
SRP007412_liver	0.00 RPM	48.32 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3721 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3721 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3721 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010062	1 retrocopy	retro_cfam_1047,
Callithrix jacchus	ENSCJAG00000017832	2 retrocopies	retro_cjac_4136, retro_cjac_4187,
Homo sapiens	ENSG00000166197	1 retrocopy	retro_hsap_4781,
Nomascus leucogenys	ENSNLEG00000015012	1 retrocopy	retro_nleu_1101,
Pongo abelii	ENSPPYG00000002595	1 retrocopy	retro_pabe_3721 ,
Pan troglodytes	ENSPTRG00000023882	1 retrocopy	retro_ptro_3182,
Tursiops truncatus	ENSTTRG00000014974	1 retrocopy	retro_ttru_155,