RetrogeneDB ID: retro_ptro_1688

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:128876829..128877335(-)
• Located in intron of: ENSPTRG00000012439

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSPTRG00000000138
• Aliases: None
• Description: None

Sequence

>retro_ptro_1688
CCTGGCTTCAATGGTCACGCTGCCATTTAGGAGGGCTGCTTCCATGAGATCTGCAGCCTGAGCCCAGGGAAGCCTTGTTG
CTACAGATGGAGCAGCTGCTCCACTGCCAGTGCTCACGCTCCCAGGATATCCTTGTTTTCCACAGTAAGACCCACAGCAG
TGTGCTGGTGTTGGATGGCATCATCCCCTGCATGGACAGGGACAAGTTCTCCTACTAGATGAGAATCAACCTGCCATTCA
GCAACCACCCCATCCCACAAAAGGTGCTGATCGTCGGGGACAAAGACGGCATCCTGCACAAGGTGGTGAAGCACCCCTCT
GTGGAGTCTGTGGTCCGATGATAGACTGAAAAGGATGGCACTCAGGTCTCTAAGAAATTCCTGCCAGGTATGGTCATTGG
CTTCTCTAGCTCTAAGCTGACCCTGCATATGGGTGACAATTTTGATTTCGTGAAGCAGAACCAGGATGCCTTCAATATTA
CGATCACTGACTCCTGGGATCCACTG

Alignment

ORF - retro_ptro_1688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.53 %
• Parental protein coverage: 56.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAASGPAAIREGWFRETCSLWPG-QALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERDE
          P...G.AAI.EG.F.E.CSL.PG..AL.LQ.EQLLH...SR.QDILVF.SKT...VLVLDG.I.C..RD.
Retrocopy PGFNGHAAI*EGCFHEICSLSPG<EALLLQMEQLLHCQCSRSQDILVFHSKTHSSVLVLDGIIPCMDRDK

Parental  FSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSS
          FSY...I.NLP...HP.P.KVLI.G..DG..L..VVKHPSVESVV......D..QVSKKFLPGM.IG.SS
Retrocopy FSY*MRI-NLPFSNHPIPQKVLIVGDKDG-ILHKVVKHPSVESVVR**TEKDGTQVSKKFLPGMVIGFSS

Parental  SKLTLHVGDGFEFMKQNQDAFDVIITDSSDPM
          SKLTLH.GD.F.F.KQNQDAF...ITDS.DP.
Retrocopy SKLTLHMGDNFDFVKQNQDAFNITITDSWDPL

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	54.73 RPM
SRP007412_cerebellum	0.04 RPM	29.18 RPM
SRP007412_heart	0.00 RPM	14.81 RPM
SRP007412_kidney	0.05 RPM	22.28 RPM
SRP007412_liver	0.03 RPM	38.66 RPM
SRP007412_testis	0.00 RPM	11.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1688 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1688 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2313
Gorilla gorilla	retro_ggor_1756

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Homo sapiens	ENSG00000116649	2 retrocopies	retro_hsap_1426, retro_hsap_2313,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Nomascus leucogenys	ENSNLEG00000009532	3 retrocopies	retro_nleu_1842, retro_nleu_2082, retro_nleu_2778,
Pongo abelii	ENSPPYG00000001892	3 retrocopies	retro_pabe_1181, retro_pabe_1828, retro_pabe_2044,
Pan troglodytes	ENSPTRG00000000138	3 retrocopies	retro_ptro_1403, retro_ptro_1688 , retro_ptro_975,