RetrogeneDB ID: retro_pabe_3531

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:4222100..4223790(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX19
• Ensembl ID: ENSPPYG00000004069
• Aliases: None
• Description: sorting nexin 19 [Source:HGNC Symbol;Acc:21532]

Sequence

>retro_pabe_3531
GAGACTCAGTTGGAGTCTCCACTGTCTGAACTAGGCTGAGAAACCATCACGCTCATGACTCCAGGCCACTTTCTGTCTGA
CAGGATTCAGGATGCCCTGTGTGTCCTAGAGGGTTCCCAGGCTCTGGAACTCAAAGATAGTGAGGGATCTGAAGGAGCAG
AGGCTGAAGAGGGTCCAGGGACAGAAACAGAGACAGGCCTGCCTGTCTCCACACTGAACTTCTGCCCAGAGATCCAGATT
GACACAGCAGACAAGGAGCTAGAACAAGGAGATGTTACCACCTCTGTTACAGCTTTGCTGGAGGGGCCGGAAAAGACCTG
CTCCTCACGGCCCTCATGCTTAGAGAAGGATCTCACCAATGATGTGAGCTACCTTGATCCTAGTCTGCCACCAGTTCTGC
TTTCCTCCTCTCCACCTGGTCCTCTCAGCTCAGCCACCTTCAGCTTTGAGCCCCTAAGCAGTCCAGATGGCCCAGTTGTC
ATCCAGAACCTTCGTATCATGGGCACCATTACAGCCCGAGAGCACAGTGGCACCAGATTGCACCCATACACACTCTATAC
TGTGAAGTATGAGACAGCCCTTGATGGTGAAAACAGCAGCAGCCTGCAGCAGCTGGCCTACCACACTGTGAATCACCGCT
ATTGGGAGTTCTTGAATCTGCAGGCCATCAGGAGAAGAAACCAGATCTATGAAAGTTCATTAAAAATGTGAAGGTTCCTA
AAAAGCTCGCTCCAGATCTTCCATTTGGAAACATGGACAGTGACAGAGTAGAGGCCCGTAAGAGCCTCTAGAATAATTCC
TGAAGCAACTGTGTGCCATTCCGGAGATCGCTAACAGTGAGGAGGTGCAGGAGTTTCTTGCTGTGAACACAGATGCTCGC
ATTTCCTTTGTCAAGAAACCATTTATGGTCTCTAGAATAGAGAAGATGGTGGTGAGTGCCATTGTGGACACCTTGAAGAC
AGCGTTTCCTTGCTCTGAATCCCAGAGCCCCACAGAGGAGCTGAGTGAGGCTGAGACTGAAAGCAAGTCCCATACAGAAG
GCAAGAAGGCTGGCAAGTCCAGACTGAGGTTCTCATCCAGTAAAATTTCTCCAGCACTAAGTGTGACTGAAGCACAAGAC
AAGATTCTTTATTGTCTCCAGGAAGGCAATGTGGAGTCCAAGACCCTATCCATGTCTGGGATGGAATCTTTTATTGAAAA
ACAGACAGTTACTGGAGATGCAGCCAACAGAAGCCCCAGTAAAAGATCCTGAACAGCTTCCCAAAGGACATGTGGACAGT
TGCTTGTCAGATGCAGCTGTGCCAGCCCAAGATCCCAGCAACAGCGATTCAGGAACAGAGACAGAGTTAATTGACACAGC
CCTGAATCTGCTTCTCTTGCTACTAACAGAACAGTGGAAATGGCTGCATACTGAAAACATGCAGAAGTTTCTTCATCTTA
TCTTTGGTACCCTAATTCAAAGGTGGCTAGAGGTGCAGGTAGCTAATTTAACAAGTCCACAGCGCTGGGTGCAGTACCTC
TGGCTTCTTCAGGAGTACATCTGGCCTGGTGGAGTTTTACCTAAGTTTCCACAGCCTGTAAGGACCCAGGAGCAGAAACT
GCCTGCTGAGAAACAGGCTTCACAGAGCCTAATGGAGTCCTCCCAGATCTCCTAGTAGAATTTCTTGGGGTGAACAAATG
CCAGCTGAGC

Alignment

ORF - retro_pabe_3531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.29 %
• Parental protein coverage: 56.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DSELESPLSELGKETIMLMTPGNFLSDGIQDALCALEGSQVLEPKDGEASEGAEAEEGPGTETETGLPVS
          ...LESPLSELG.ETI.LMTPG.FLSD.IQDALC.LEGSQ.LE.KD.E.SEGAEAEEGPGTETETGLPVS
Retrocopy ETQLESPLSELG*ETITLMTPGHFLSDRIQDALCVLEGSQALELKDSEGSEGAEAEEGPGTETETGLPVS

Parental  TLNSCPEIHIDTADEEIEQGDVTASVTALLEGPEKTCPSRPSCLEKDLTNDVSSLDPTLPPVLLSSSPPG
          TLN.CPEI.IDTAD.E.EQGDVT.SVTALLEGPEKTC.SRPSCLEKDLTNDVS.LDP.LPPVLLSSSPPG
Retrocopy TLNFCPEIQIDTADKELEQGDVTTSVTALLEGPEKTCSSRPSCLEKDLTNDVSYLDPSLPPVLLSSSPPG

Parental  PLSSATFSFEPLSSPDGPVIIQNLRITGTITAREHSGAGFHPYTLYTVKYETALDGEKSSGLQQLAYHTV
          PLSSATFSFEPLSSPDGPV.IQNLRI.GTITAREHSG...HPYTLYTVKYETALDGE.SS.LQQLAYHTV
Retrocopy PLSSATFSFEPLSSPDGPVVIQNLRIMGTITAREHSGTRLHPYTLYTVKYETALDGENSSSLQQLAYHTV

Parental  NRRYREFLNLQT-RLEEKPDLRKFIKNVKGPKKLFPDLPFGNMDSDRVEARKSL-LESFLKQLCAIPEIA
          N.RY.EFLNLQ....E.KPDL.KFIKNVK.PKKL.PDLPFGNMDSDRVEARKSL.LE.FLKQLCAIPEIA
Retrocopy NHRYWEFLNLQA<HQEKKPDL*KFIKNVKVPKKLAPDLPFGNMDSDRVEARKSL<LE*FLKQLCAIPEIA

Parental  NSEEVQEFLALNTDARIAFVKKPFMVSRIDKMVVSAIVDTLKTAFPRSEPQSPTEELSEAETESKSQTEG
          NSEEVQEFLA.NTDARI.FVKKPFMVSRI.KMVVSAIVDTLKTAFP.SE.QSPTEELSEAETESKS.TEG
Retrocopy NSEEVQEFLAVNTDARISFVKKPFMVSRIEKMVVSAIVDTLKTAFPCSESQSPTEELSEAETESKSHTEG

Parental  KKASKSRLRFSSSKISPALSVTEAQDKILYCLQEGNVESETLSMSGMESFIEKQTKLLEMQPTKAPGK-D
          KKA.KSRLRFSSSKISPALSVTEAQDKILYCLQEGNVES.TLSMSGMESFIEKQT..........P.K.D
Retrocopy KKAGKSRLRFSSSKISPALSVTEAQDKILYCLQEGNVESKTLSMSGMESFIEKQT-VTGDAANRSPSK>D

Parental  PEQPPKGRVDSCVSDAAVPAQDPGNSDPGTETELADTALDLLLLLLTEQWKWLCTENMQKFLRLIFGTLV
          PEQ.PKG.VDSC.SDAAVPAQDP.NSD.GTETEL.DTAL.LLLLLLTEQWKWL.TENMQKFL.LIFGTL.
Retrocopy PEQLPKGHVDSCLSDAAVPAQDPSNSDSGTETELIDTALNLLLLLLTEQWKWLHTENMQKFLHLIFGTLI

Parental  QRWLEVQVANLTSPQRWVQYLRLLQESIWPGGVLPKFPRPVRTQEQKLAAEKQALQSLM-GVLPDLIVEI
          QRWLEVQVANLTSPQRWVQYL.LLQE.IWPGGVLPKFP.PVRTQEQKL.AEKQA.QSLM.GVLPDL.VE.
Retrocopy QRWLEVQVANLTSPQRWVQYLWLLQEYIWPGGVLPKFPQPVRTQEQKLPAEKQASQSLM<GVLPDLLVEF

Parental  LRVNKCQLS
          L.VNKCQLS
Retrocopy LGVNKCQLS

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	102.84 RPM
SRP007412_cerebellum	0.00 RPM	68.34 RPM
SRP007412_heart	0.00 RPM	37.33 RPM
SRP007412_kidney	0.00 RPM	60.72 RPM
SRP007412_liver	0.03 RPM	31.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3531 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3531 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3531 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000120451	2 retrocopies	retro_hsap_1235, retro_hsap_1919,
Pongo abelii	ENSPPYG00000004069	1 retrocopy	retro_pabe_3531 ,
Pan troglodytes	ENSPTRG00000004487	3 retrocopies	retro_ptro_1243, retro_ptro_3076, retro_ptro_849,