RetrogeneDB ID: retro_pabe_2577

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:172062283..172064682(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOL8
• Ensembl ID: ENSPPYG00000019375
• Aliases: None
• Description: nucleolar protein 8 [Source:RefSeq peptide;Acc:NP_001127235]

Sequence

>retro_pabe_2577
CCAGGGTATAAGAATTGGGTTGTGAGAAAATTTGGAAGACTGTTACTTGTTCTTCACCTTAAAAATTATCATAAATGTAA
AATTATAAAATATGATCCCTCAAAATACTGCCACAACCTAAAGAAGTAGGGGAGGATTTCACAAACGCCATTCCTATATC
CATCCTGACTTGTGAACTGGAAGGAGGGAATGATCCTATGAGTAAGAAATGGTGAGGAGACTTCTCTGACTTTCATGACC
CTCCCAAGAAGGTGATAAAAGTGCAGAAGGATGAGAGTTCCACTGGGTCTCTGGCCATGAGTCCAAGGCTCAGGTGGGTA
ATAGAGAGACCACACTTAACACAGCAACAAGCTGCACAAAAAAAGAACTTCTAATTCCGCTACTCCTAAATTATCTCCTA
TACCTGTTTCTGATACTCAGAAACTTTAAAATCTACCCTTTAGGACTTCTGGATTGGAAACTGCCAAGAAGAGAAATGGC
ATTTCTGATATGATATTGATTCCAAAGATGAATTAAGAATGATGGTTGCAAAAGAGGAAAACTTACAGAGAACTACACAA
TTCTCAATAAATGAATCTGAAAATGATCCCTTTGAAGTTGTAAAGGATGATTTCAAATCAGGAGTTCACAAATTGCATTC
TTCCACAGGTTTAGGTATCAAAAATAATGTCTCTTGCCATGACAGTGATGATGATATTACGAGAAATGATTGTGAGTATG
ACTCAGGAGATACAGATGAAATCATTGCGATGAAAAAAAAATGTTGCTAAGGTCAAAAACAGTACAGAATTTTCACAAAT
GGAAAAATCTACAGACAAGAAAACTTCCTCCAAAAATAGAGAAAACTGTGACCTTTCTGATCACTGTATTAAAGTACAAA
AAAGAAAAAGCAATGTAGAGTCAGCCTTTGGTCGTGGATTAAAGGCTCTTAATCGCAAATCTCCCTCTCACTCCAATAGC
AATGAAGATGCTGATTCTGCATCAGAATTAGCTGACTCTGAAGGAGACAAGGAGTATAATGCCATAATGAAAAACCACCT
TCATGTGAATCTCACTTTAGCTGATTTGGAACAATTGGCTGGCAGTGAACAGAAGGTTTCCAATGAAGATACTGAGAGTG
ACGGACCAGAAACCACCACACAATGCAAGTCTGACAGAGGCTCCAACAGCCCCAAGACTCCCACTGGCCTCCACAGACGC
AGACACTGTATTTGTCCTGAGGACACTGTGGCTTCCCTGTTAGAAGGAGAGGAGAGCACCTGTGGCAAACAGAAACCAAA
GGAAAACAACTGAAAGCCAGAATTCCAGGTTTTCAAGGGAGTAGGCTGTTTATATGAAAAAAGAGTCAATAAAAAAATCC
TTGAAAGACAATGTTGCCTCTAACAATATTAATAAAGATAAGAATTCCATGAAACATGTGGATCCCAGGATCATATCCAT
GGAAGATGGGTCCCCATATGTTAATGGCTCATTGGGTGAACTGACTCTGTGCCAACATGCAAAGAAGGCAAATGGCCCAA
ACTATATTCAGCTTCAAAAAAGACAGAACACTTCTGAGAGCCAGGATTGCAAGGCAGTGTCCACTAGCAGTTCTAAAAAG
AGAAGTAAGAATTCTATTTCTAGTTTATTGCCATTAAAAGATAAGAAGTCCTTAAGTCTTAGTGCAAAGTCTCACAACAT
AGGCTTTGACACAACAGCTGCCATAGTACCACAAAGACAGAAGCTTCAGAGGAAGAGAGGTCTAATTCAAGCAGCCTCAC
ATCTCTTGAGAAATCACCAAAGGTCTCATCCAAGGACACTCAGGAAATCAAAACTGATTTCTCACTTTCTATTAGTAATT
CATCAGATCTGAGTGCTAAGGATAAACATGCTGAAGACGACGAGAAGCATTTGGCAGTCTTGGAAGTGAGGCAAAAAGCA
AAAGAAGTGCAGAAGAAGCCGGTGCATAATGATCTGGCAAATTTGGATGGTCATCTAGAGGATAAACTAACATACATCAT
CTTCGGTTCTGACAGTGAATGTGAAACAGAGGAGATATCAACTCAGGAGCAGAGCCATCCAGGAGAGGAATGGGTGGAAG
AGTCTATGGGTAAAACATCGGGGAAGCTGCCTGATAGCAGTGATGACGAGGAATCTGATTCTGAAGATGACAGTAAAAGG
TTCAAAATTAAACCTCAGTTTGAGGGCAGAGCTGGACAGAAGCTCGTGGATTTATAGTCACACTTTGGCACTGATGACAG
ATTCTGCATGAATTCTCAATTTCTAGAAAGTGACAGTGAAGAGGAACAGGAAGAGGTAAATGAAAAGAAACCTGCTAGGA
AGAAGAGCTTGCTGAAGAAAAAAAGAAAGCCCTGGATGTTGTACAAAGTGTTTTGAAAATCAACTTAAGCAATTCTACA

Alignment

ORF - retro_pabe_2577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.43 %
• Parental protein coverage: 68.21 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  PGHKNWVVSKFGRVLPVLHLKNQHKRKVIKYDPSKYCHNLKK-IGEDFSNTIPISSLTWELEGGNDPMSK
          PG.KNWVV.KFGR.L.VLHLKN.HK.K.IKYDPSKYCHNLKK..GEDF.N.IPIS.LT.ELEGGNDPMSK
Retrocopy PGYKNWVVRKFGRLLLVLHLKNYHKCKIIKYDPSKYCHNLKK<VGEDFTNAIPISILTCELEGGNDPMSK

Parental  KRRGEFSDFHGPPKKIIKVQKDESSTGSLAMSTRPRRVIERPPLTQQQAAQK-RTCDSITPSKSSPVPVS
          K..G.FSDFH.PPKK.IKVQKDESSTGSLAMS.R.R.VIERP.LTQQQAAQK.RT..S.TP.K.SP.PVS
Retrocopy KW*GDFSDFHDPPKKVIKVQKDESSTGSLAMSPRLRWVIERPHLTQQQAAQK>RTSNSATP-KLSPIPVS

Parental  DTQKLKNLPFKTSGLKTAKKRNSISDD-DTDSEDELRMMIAKEENLQRTTQPSINESENDPFEVVRDDFK
          DTQKL.NLPF.TSGL.TAKKRN.ISD..D.DS.DELRMM.AKEENLQRTTQ.SINESENDPFEVV.DDFK
Retrocopy DTQKL*NLPFRTSGLETAKKRNGISDM<DIDSKDELRMMVAKEENLQRTTQFSINESENDPFEVVKDDFK

Parental  SGVHKLHSLIGLGIKNNVSCHDSDDDDTRNDCEYDSGDTDEIIVMKKN-VAKVKNSTEFSQMEKST-KKT
          SGVHKLHS..GLGIKNNVSCHDSDDD.TRNDCEYDSGDTDEII.M....VAKVKNSTEFSQMEKST.KKT
Retrocopy SGVHKLHSSTGLGIKNNVSCHDSDDDITRNDCEYDSGDTDEIIAMXXX>VAKVKNSTEFSQMEKSTDKKT

Parental  SFKNRENCELSDHCIKLQKRKSNVESALSHGLKSLNCKSPSHSSSSEDADSASELADSEGGEEYNAMTKN
          S.KNRENC.LSDHCIK.QKRKSNVESA...GLK.LN.KSPSHS.S.EDADSASELADSEG..EYNA..KN
Retrocopy SSKNRENCDLSDHCIKVQKRKSNVESAFGRGLKALNRKSPSHSNSNEDADSASELADSEGDKEYNAIMKN

Parental  CLRVNLTLADLEQLAGSDLKVPNEDTESDGPETTTQCKFDRGSKSPKTPTGLRRGRQCIRPEEIVASLLE
          .L.VNLTLADLEQLAGS..KV.NEDTESDGPETTTQCK.DRGS.SPKTPTGL.R.R.CI.PE..VASLLE
Retrocopy HLHVNLTLADLEQLAGSEQKVSNEDTESDGPETTTQCKSDRGSNSPKTPTGLHRRRHCICPEDTVASLLE

Parental  GEENNCGKQKPKENNLKPKFQAFKGVGCLYE-KESMKKSLKDSVASNNINKDQNSMKHEDPSIISMEDGS
          GEE..CGKQKPKENN.KP.FQ.FKGVGCLYE.KES.KKSLKD.VASNNINKD.NSMKH.DP.IISMEDGS
Retrocopy GEESTCGKQKPKENN*KPEFQVFKGVGCLYE>KESIKKSLKDNVASNNINKDKNSMKHVDPRIISMEDGS

Parental  PYVNGSSGEVTPCEHTKKANGPNYIQPQKRQTTFESQDHKAVSPRSSEKRSKNPISR--PLEGKKSLSLS
          PYVNGS.GE.T.C.H.KKANGPNYIQ.QKRQ.T.ESQD.KAVS..SS.KRSKN.IS...PL..KKSLSLS
Retrocopy PYVNGSLGELTLCQHAKKANGPNYIQLQKRQNTSESQDCKAVSTSSSKKRSKNSISSLLPLKDKKSLSLS

Parental  AKTHNIGFD-KDSCHSTTKTEASEEERSDSSSLTSLKKSPKVSSKDTREIKTDFSLSISNSSDLSAKDKH
          AK.HNIGFD...SCHSTTKTEASEEERS.SSSLTSL.KSPKVSSKDT.EIKTDFSLSISNSSDLSAKDKH
Retrocopy AKSHNIGFD<HNSCHSTTKTEASEEERSNSSSLTSLEKSPKVSSKDTQEIKTDFSLSISNSSDLSAKDKH

Parental  AEDNEKRLAALEARQKEKEVQKQLVHNALANLDGHPEDKPTHIIFGSDSECETEETSTQEQSHPGEEWVK
          AED.EK.LA.LE.RQK.KEVQK..VHN.LANLDGH.EDK.T.IIFGSDSECETEE.STQEQSHPGEEWV.
Retrocopy AEDDEKHLAVLEVRQKAKEVQKKPVHNDLANLDGHLEDKLTYIIFGSDSECETEEISTQEQSHPGEEWVE

Parental  ESMGKTSGKLFDSS-DEESDSEDDSNRFKIKPQFEGRAGQKLMDLQSHFGTDDRFRMDSRFLETDSEEEQ
          ESMGKTSGKL.DSS.DEESDSEDDS.RFKIKPQFEGRAGQKL.DL.SHFGTDDRF.M.S.FLE.DSEEEQ
Retrocopy ESMGKTSGKLPDSSDDEESDSEDDSKRFKIKPQFEGRAGQKLVDL*SHFGTDDRFCMNSQFLESDSEEEQ

Parental  EEVNEKKTEE-EE-LAEEKKKALNVIQSVLQINLSNST
          EEVNEKK....EE.LAEEKKKAL.V.QSVL.INLSNST
Retrocopy EEVNEKKPAR<EEELAEEKKKALDVVQSVLKINLSNST

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	17.25 RPM
SRP007412_cerebellum	0.00 RPM	21.16 RPM
SRP007412_heart	0.00 RPM	10.72 RPM
SRP007412_kidney	0.00 RPM	18.89 RPM
SRP007412_liver	0.03 RPM	20.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2577 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2577 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3121
Pan troglodytes	retro_ptro_2110

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000198000	1 retrocopy	retro_hsap_3121,
Nomascus leucogenys	ENSNLEG00000016357	1 retrocopy	retro_nleu_773,
Pongo abelii	ENSPPYG00000019375	1 retrocopy	retro_pabe_2577 ,
Pan troglodytes	ENSPTRG00000021109	1 retrocopy	retro_ptro_2110,