RetrogeneDB ID: retro_pabe_1668

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:23036042..23036887(-)
• Located in intron of: ENSPPYG00000009794

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX6
• Ensembl ID: ENSPPYG00000005736
• Aliases: None
• Description: sorting nexin 6 [Source:HGNC Symbol;Acc:14970]

Sequence

>retro_pabe_1668
GCAGCCATGATGGAAGACCTGGACGATGGCCCTGACTTCCTCTTGGGAAGAGAACCGTGGACTTAAAGCAATAAATGTAG
ATCTTCAAAGTGATCCTGCTCTGCAGGTGGACATTTCTGATGCTCTTAGTGAGTGGGATAAAGTAAAACTCACTGTTCAC
ACAAAGAGTTTATTGCCAAATTTTAAACAAAATAAGTTTTCTGTTGTTCAGAAACATGAGAAATTTATCTGGCTTCATGA
TTCCTTTCTTAAAAATGAAGACTATGCAGGTTACATCATTCCACCAGCACGACCAAGACCTGATTTTGATGCTTCAAGGG
AAAAAGTACAGAAGCTTGGAGAAGAAGAAGGATCAATGACAAAGGAAGAATTCACAAAGATAAAAACAGGAACTGGAAGC
TGAATATTTGGGAATATTCGAGAAGACAGTTGCGATGCATGAAGTGTTCCTATGTCATGTGACAGCACATCCTATTTTGA
GAAAATATTTAAATTTCCATGTCTTCTTGGGATATAATCAAGATTTGAGTGTGCAAGGAAAAATAAAAAGAGAAACTTGA
AGATTTCTTTGAAAACATGGTTAAATCACCAGATGGAGTAATTGTTTCAGAAGTAAAGGATGTAGATAATTTCTTTCAGC
ATGAACAAACATTTCTTTTAGAATATCATAACCAAGTTAAGGATGCATCTGCTAAGGAATCATGAATGACAAGATCCCAC
AAAAGTGCTGCAGATGATTACAATAGAATTGGTTCTTCATTATATGCTTTAGGAAATCAGGATTCACAGATATATGCAAG
TTTTTTCTCAAAGTTTCAGAAGTGTTTGATAAAACAAGAAAAATA

Alignment

ORF - retro_pabe_1668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.02 %
• Parental protein coverage: 72.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AAMMEGLDDGPDFLS-EEDRGLKAINVDLQSDAALQVDISDALSERDKVKFTVHTKSSLPNFKQNEFSVV
          AAMME.LDDGPDFL..EE.RGLKAINVDLQSD.ALQVDISDALSE.DKVK.TVHTKS.LPNFKQN.FSVV
Retrocopy AAMMEDLDDGPDFLL>EENRGLKAINVDLQSDPALQVDISDALSEWDKVKLTVHTKSLLPNFKQNKFSVV

Parental  RQHEEFIWLHDSFVENEDYAGYIIPPAPPRPDFDASREKLQKLGEGEGSMTKEEFTKM-KQELEAEYLAI
          ..HE.FIWLHDSF..NEDYAGYIIPPA.PRPDFDASREK.QKLGE.EGSMTKEEFTK..KQELEAEYL.I
Retrocopy QKHEKFIWLHDSFLKNEDYAGYIIPPARPRPDFDASREKVQKLGEEEGSMTKEEFTKI>KQELEAEYLGI

Parental  FKKTVAMHEVFLCRVAAHPILRKDLNFHVFLEYNQDLSVRG-KNK-KEKLEDFFKNMVKSADGVIVSGVK
          F.KTVAMHEVFLC.V.AHPILRK.LNFHVFL.YNQDLSV.G.KNK.KEKLEDFF.NMVKS.DGVIVS.VK
Retrocopy FEKTVAMHEVFLCHVTAHPILRKYLNFHVFLGYNQDLSVQG<KNK<KEKLEDFFENMVKSPDGVIVSEVK

Parental  DVDDFFEHERTFLLEYHNRVKDASAKSDRMTRSHKSAADDYNRIGSSLYALGTQDS-TDICKFFLKVSEL
          DVD.FF.HE.TFLLEYHN.VKDASAK...MTRSHKSAADDYNRIGSSLYALG.QDS.TDICKFFLKVSE.
Retrocopy DVDNFFQHEQTFLLEYHNQVKDASAKES*MTRSHKSAADDYNRIGSSLYALGNQDS<TDICKFFLKVSEV

Parental  FDKTRDL
          FDKTR..
Retrocopy FDKTRKI

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	7.13 RPM
SRP007412_cerebellum	0.00 RPM	12.89 RPM
SRP007412_heart	0.00 RPM	7.83 RPM
SRP007412_kidney	0.00 RPM	16.54 RPM
SRP007412_liver	0.00 RPM	10.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1668 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1668 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012873	1 retrocopy	retro_btau_870,
Cavia porcellus	ENSCPOG00000006862	1 retrocopy	retro_cpor_1145,
Nomascus leucogenys	ENSNLEG00000003310	1 retrocopy	retro_nleu_3063,
Pongo abelii	ENSPPYG00000005736	2 retrocopies	retro_pabe_1668 , retro_pabe_1698,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442, retro_pabe_877,
Pan troglodytes	ENSPTRG00000006253	1 retrocopy	retro_ptro_1362,