RetrogeneDB ID: retro_ptro_2082

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:120236141..120237015(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000019067
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NT5C3B
• Ensembl ID: ENSPTRG00000009181
• Aliases: None
• Description: 5'-nucleotidase, cytosolic IIIB [Source:HGNC Symbol;Acc:28300]

Sequence

>retro_ptro_2082
AAAAGTTCAGTTCGAATCAAGAACCTTACAAGAGTAGAAGAAATGATCTGTGGTCTTATCAAAGGAGGAGCTGCCAAACT
TCAGATAATAACGGACTTTGATATGACACTCAGTAGATTTTCATACAAAGGGAAAAGATGCCCAACATGTCATAATAGCA
TTGACAACTGTCAGCTGGTTACAGATGAATGCAGAAAAAAGTTATTGCAACTAAAGAAAAAATATTACGCTATTGAAGTT
GATCCTGTTCTTACTGTAGAAGAGAAGTACCCTTATATGGTGGAATGGTATACTAAATCACATGGTTTGCTTGTTCAACA
AGCTTTACCAAAAGCTAAACTTAAAGAAATTGTGGCAGAATCTGACGTTATGCTCAAAGAAAGATATGAAGAATTTCTTT
GATAAGCTCCAACAACATAGTATCCCCGTGTTCATATTTTCGGCTGGAATCAGCGATGTACTAGAGGAGGTTATTCGTCA
AGCTGGTGTTTATCATCCAAATGTCAAAGTTGTGTCCAATTTTATGGATTTTGATGAAACTGGGGTGCTCAAAGGATTTA
AAGGAGTTCTAATTCATATATTTAACAAACATGATGGTGCCTTGAGGAATACAGAATATTTCAATCAACTAAAAGACAAT
AGTAACATAATTCTTCTGGGAGACTCCCAAGGAGACTTAAGAATGGCAGATGGAGTGGCCAATGTTGAGCACATTCTGAA
AATTGGATATCTAAATGACAGAGTGGATGAGCTTTTAGAAAAGTACATGGACTCTTATGATATTGTTTTAGTACAAGATG
AATCATTAGAAGTAGCCAACTCTATTTTACAGAAGATTCTATAAACAAGCATTCTCCAAGAAGACCTCTCTCCT

Alignment

ORF - retro_ptro_2082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.14 %
• Parental protein coverage: 97. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KATVLMRQPGRVQEIVGALRKGGGDRLQVISDFDMTLSRFAYNGKRCPSSYNILDNSKIISEECRKELTA
          K..V......RV.E....L.KGG...LQ.I.DFDMTLSRF.Y.GKRCP...N..DN......ECRK.L..
Retrocopy KSSVRIKNLTRVEEMICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNSIDNCQLVTDECRKKLLQ

Parental  LLHHYYPIEIDPHRTVKEKLPHMVEWWTKAHNLLCQQKIQKFQIAQVVRESNAMLREGY-KTFFNTLYHN
          L...YY.IE.DP..TV.EK.P.MVEW.TK.H.LL.QQ...K......V.ES..ML.E.Y.K.FF..L...
Retrocopy LKKKYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKERY>KNFFDKLQQH

Parental  NIPLFIFSAGIGDILEEIIRQMKVFHPNIHIVSNYMDFNEDGFLQGFKGQLIHTYNKNSSACENSGYFQQ
          .IP.FIFSAGI.D.LEE.IRQ..V.HPN...VSN.MDF.E.G.L.GFKG.LIH..NK...A..N..YF.Q
Retrocopy SIPVFIFSAGISDVLEEVIRQAGVYHPNVKVVSNFMDFDETGVLKGFKGVLIHIFNKHDGALRNTEYFNQ

Parental  LEGKTNVILLGDSIGDLTMADGVPGVQNILKIGFLNDKVEERRERYMDSYDIVLEKDETLDVVNGLLQHI
          L....N.ILLGDS.GDL.MADGV..V..ILKIG.LND.V.E..E.YMDSYDIVL..DE.L.V.N..LQ.I
Retrocopy LKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVQDESLEVANSILQKI

Parental  LCQGVQLEMQGP
          L......E...P
Retrocopy L*TSILQEDLSP

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	0.43 RPM	41.74 RPM
SRP007412_cerebellum	0.57 RPM	37.93 RPM
SRP007412_heart	0.85 RPM	6.82 RPM
SRP007412_kidney	0.89 RPM	23.98 RPM
SRP007412_liver	0.13 RPM	10.93 RPM
SRP007412_testis	0.84 RPM	97.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2082 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2082 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2082 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3084
Gorilla gorilla	retro_ggor_2119

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013493	1 retrocopy	retro_eeur_413,
Pan troglodytes	ENSPTRG00000009181	1 retrocopy	retro_ptro_2082 ,
Sorex araneus	ENSSARG00000006434	1 retrocopy	retro_sara_505,