RetrogeneDB ID: retro_ptro_1920

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:122901100..122901560(-)
• Located in intron of: ENSPTRG00000015256

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSRP1
• Ensembl ID: ENSPTRG00000001836
• Aliases: None
• Description: None

Sequence

>retro_ptro_1920
ATGGTTTGCAGGAAAAATTTAGATAGCACAACAGTGGCAATTCACAATGAAGAGATCTACTGCAAATCCTACTATGGAAA
GAAATATGGGACAAAAGGCTATGGTTATGGCCAGGGTGCTGGCACGCTTAACATGGCGAGAGGCTGGGCATCAAGCCAGA
GAGTGTTCAGCCTCACAGGCCTACAACAAATCCAAATGCTTCTGAATTTGCTCAGAAATATGGAGGTGCTGAGAAGTGTT
CCAGATGTGGGGATTCTGTATATGCTGCCGAGAAGATAATTGGAGCTGGAAAGCCCTGGCACAAAAACTGTTTCTGATGT
GCAAAGTGTGGGAAGAGTCTTGAATCAACAACTCTGACTGAAAAAGAAGGTGAAATCTATTGTAATGGTGCTATGCAAAG
AACTTTGGGCCCAAGGGATTTGGCTATGGCCAAGGAGCAGGGGCTCTTGTTCATGCCCAG

Alignment

ORF - retro_ptro_1920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.78 %
• Parental protein coverage: 80.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVCKKNLDSTTVAVHGEEIYCKSCYGKKYGPKGYGYGQGAGTLSTDK-GESLGIKHEEAPGHRPTTNPNA
          MVC.KNLDSTTVA.H.EEIYCKS.YGKKYG.KGY..G.G.G.......GE.LGIK.E....HRPTTNPNA
Retrocopy MVCRKNLDSTTVAIHNEEIYCKSYYGKKYGTKGY--GYGQGAGTLNM<GERLGIKPESVQPHRPTTNPNA

Parental  SKFAQKIGGSERCPRCSQAVYAAEKVIGAGKSWHKACFRCAKCGKGLESTTLADKDGEIYCKG-CYAKNF
          S.FAQK.GG.E.C.RC...VYAAEK.IGAGK.WHK.CF.CAKCGK.LESTTL..K.GEIYC.G.CYAKNF
Retrocopy SEFAQKYGGAEKCSRCGDSVYAAEKIIGAGKPWHKNCF*CAKCGKSLESTTLTEKEGEIYCNG<CYAKNF

Parental  GPKGFGFGQGAGALVHSE
          GPKGFG.GQGAGALVH..
Retrocopy GPKGFGYGQGAGALVHAQ

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	0.09 RPM	264.70 RPM
SRP007412_cerebellum	0.04 RPM	172.32 RPM
SRP007412_heart	0.06 RPM	61.56 RPM
SRP007412_kidney	0.13 RPM	277.39 RPM
SRP007412_liver	0.07 RPM	95.81 RPM
SRP007412_testis	0.11 RPM	15.39 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1920 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1920 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1920 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2833
Gorilla gorilla	retro_ggor_1967
Pongo abelii	retro_pabe_2199
Macaca mulatta	retro_mmul_1505

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012114	1 retrocopy	retro_amel_1294,
Echinops telfairi	ENSETEG00000017067	1 retrocopy	retro_etel_417,
Macaca mulatta	ENSMMUG00000020772	1 retrocopy	retro_mmul_1505,
Mus musculus	ENSMUSG00000026421	1 retrocopy	retro_mmus_2226,
Pan troglodytes	ENSPTRG00000001836	2 retrocopies	retro_ptro_1920 , retro_ptro_1922,
Pan troglodytes	ENSPTRG00000033768	1 retrocopy	retro_ptro_43,
Tupaia belangeri	ENSTBEG00000008991	1 retrocopy	retro_tbel_2176,
Drosophila melanogaster	FBgn0259209	1 retrocopy	retro_dmel_71,