RetrogeneDB ID: retro_ptro_1922

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:134381995..134382467(-)
• Located in intron of: ENSPTRG00000015390

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_1922
CACCGCTGCTGCTTTCTATGCATGATTTGCAGGAATAATTTAGATAGCAAGACAGTGGCAATTCATGATTAAGAGATTTA
CTGCAAATCCTGCTATGGAAAGAAGTATGGGCCAAAAGGCTACAGTTTACGGCCAGGGCGCTGGCATATTTAACATGGAC
CGTGGTGAGAGCCTGGGCATCAAGCCAGAGTGTTCAGCCTCACATGCCTACAAACAAATCCAAAGACTTCTAAATTTGCT
CAGAAATACAGAGGTGCTGAGAAGTGTTCCAGATGTGGGGATTCCGTACATGCTGCTGAGAAGGTAACTGGAGCTGGAAA
GCCCTGGAACAAAAACTATTTCCGATGTGCAAAGTGTGGGAAGAGTCTTGAATCAACAACTCCTGACTGAAAAAGAAGGT
GAAATCTATTGTAAAGGGTGCTATGCAAAGAACTTTGGGCCCAAGGGATTTGGCTATGGCCAAGGAGAGGGC

Alignment

ORF - retro_ptro_1922 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 81.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HKSCFLCMVCKKNLDSTTVAVHGEEIYCKSCYGKKYGPKGYG-YGQGAGTLSTDKGESLGIKHEEAPGHR
          H..CFLCM.C..NLDS.TVA.H..EIYCKSCYGKKYGPKGY..YGQGAG....D.GESLGIK.E....H.
Retrocopy HRCCFLCMICRNNLDSKTVAIHD*EIYCKSCYGKKYGPKGYS>YGQGAGIFNMDRGESLGIKPECSASHA

Parental  PT-TNPNASKFAQKIGGSERCPRCSQAVYAAEKVIGAGKSWHKACFRCAKCGKGLESTT-LADKDGEIYC
          ...TNP..SKFAQK..G.E.C.RC...V.AAEKV.GAGK.W.K..FRCAKCGK.LESTT.L..K.GEIYC
Retrocopy YK<TNPKTSKFAQKYRGAEKCSRCGDSVHAAEKVTGAGKPWNKNYFRCAKCGKSLESTT>LTEKEGEIYC

Parental  KGCYAKNFGPKGFGFGQGAG
          KGCYAKNFGPKGFG.GQG.G
Retrocopy KGCYAKNFGPKGFGYGQGEG

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	264.70 RPM
SRP007412_cerebellum	0.04 RPM	172.32 RPM
SRP007412_heart	0.00 RPM	61.56 RPM
SRP007412_kidney	0.03 RPM	277.39 RPM
SRP007412_liver	0.00 RPM	95.81 RPM
SRP007412_testis	0.00 RPM	15.39 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1922 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1922 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1922 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2836
Pongo abelii	retro_pabe_2347
Macaca mulatta	retro_mmul_1474

---

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,