RetrogeneDB ID: retro_ptro_1362

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:23135057..23135758(-)
• Located in intron of: ENSPTRG00000023170

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX6
• Ensembl ID: ENSPTRG00000006253
• Aliases: None
• Description: None

Sequence

>retro_ptro_1362
GGAGCAGCCATGATGGAAGACTTGGACGATGGCCCTGACTTCCTCTTGGGAAGAGAACCGTGGACTTAAAGCAATAAATG
TAAACCTTCAAAGTGATCCTGCTCTGCTGGTGGACATTTCTGATGCTCTTAGTGAGTGGAATAAAGTAAAATTCACCGTT
CACACAAAGAGTTTATTTCCAAATTTTAAACAAAATGAGTTTTCTGTTGTTCAGCAACGTGAGCAATTTATCTGGCTTCA
TGATTCCTTTGTTAAAAATGAAGACTATGCAGGTTACATCATTCCACCAGCACCACCAAGAGCTGATTTTGATGCTTCAA
GGGAAAAAGTACAGAAGCTTGGAGAAGGAGAAGGGTCAATGACAAAGGAAGAATTCACAAAGATGAAACAGGAAGTGGAA
GCTGGATATTTGGGAATATCCAAGAACACAGTTGTGATGCATGAAGTGTTCCTATGTCATGTGACAGCACATCCTATTTT
GAGAAAATATTTAAATTTCCATGTCTTCTTGGAATATAATCAAGACTTGAGTGTGCAAGGAAAAATAAAAAGAGAAACTT
GAAGATTTCTTTAAAAACATGGTTAAATCAGCAGATGGAGTAATTGTTTCCAGAGTAAAGGATGTAGATAATTTCTTTGA
GCATGAACAAACATTTCTTTTAGAATATCATAACCGAGATAAGGATGCATCTGCTAACTCA

Alignment

ORF - retro_ptro_1362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.65 %
• Parental protein coverage: 55.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAAMMEGLDDGPDFLS-EEDRGLKAINVDLQSDAALQVDISDALSERDKVKFTVHTKSSLPNFKQNEFSV
          GAAMME.LDDGPDFL..EE.RGLKAINV.LQSD.AL.VDISDALSE..KVKFTVHTKS..PNFKQNEFSV
Retrocopy GAAMMEDLDDGPDFLL>EENRGLKAINVNLQSDPALLVDISDALSEWNKVKFTVHTKSLFPNFKQNEFSV

Parental  VRQHEEFIWLHDSFVENEDYAGYIIPPAPPRPDFDASREKLQKLGEGEGSMTKEEFTKMKQELEAEYLAI
          V.Q.E.FIWLHDSFV.NEDYAGYIIPPAPPR.DFDASREK.QKLGEGEGSMTKEEFTKMKQE.EA.YL.I
Retrocopy VQQREQFIWLHDSFVKNEDYAGYIIPPAPPRADFDASREKVQKLGEGEGSMTKEEFTKMKQEVEAGYLGI

Parental  FKKTVAMHEVFLCRVAAHPILRKDLNFHVFLEYNQDLSVRG-KNK-KEKLEDFFKNMVKSADGVIVSGVK
          .K.TV.MHEVFLC.V.AHPILRK.LNFHVFLEYNQDLSV.G.KNK.KEKLEDFFKNMVKSADGVIVS.VK
Retrocopy SKNTVVMHEVFLCHVTAHPILRKYLNFHVFLEYNQDLSVQG<KNK<KEKLEDFFKNMVKSADGVIVSRVK

Parental  DVDDFFEHERTFLLEYHNRVKDASAKS
          DVD.FFEHE.TFLLEYHNR.KDASA.S
Retrocopy DVDNFFEHEQTFLLEYHNRDKDASANS

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	17.57 RPM
SRP007412_cerebellum	0.00 RPM	15.45 RPM
SRP007412_heart	0.00 RPM	30.49 RPM
SRP007412_kidney	0.00 RPM	26.94 RPM
SRP007412_liver	0.00 RPM	11.72 RPM
SRP007412_testis	0.11 RPM	25.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1362 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1362 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1362 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,
Pan troglodytes	ENSPTRG00000006253	1 retrocopy	retro_ptro_1362 ,
Pan troglodytes	ENSPTRG00000013278	2 retrocopies	retro_ptro_2052, retro_ptro_717,