RetrogeneDB ID: retro_ptro_1617

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:81232119..81232880(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM7
• Ensembl ID: ENSPTRG00000004305
• Aliases: None
• Description: None

Sequence

>retro_ptro_1617
TTTGTGGGCAACCTTGAAACGAAAGTGACCGAGGAGCTCCTTTTCGAGCTTTTCCACCAGGCTGGGCCAGTAATAAAGGT
GAAATTCCAAAAGATAAGGATGGTAAACCAAAGCAGTTTGCGTTTGTGAATTTCAAACATGAAGTATCTGTTCCTTATGC
AATGAATCTACTTAATGGAATCAAACTTTACGGAAGGCCTATCAAAATTCAATTTAGATCAGGAAGTAGTCATGCCTTGC
AAGATGTCAGTTTGCCATATCCCCAACATCATGTTGGAAATTCAAGCCCTACCTCCACATCTCCTAGCAGGTACGAAAGG
ACTAGGGATAACATGACTTCATCAGCACAGATAATTCAGAGATCTTTCTCTTCTCCAGAAAATTTTCAGAGACAAGCAGT
GATGAACAGTGCTTTGAGACAAATGTCATATGGTGGAAAATTTGGTTCTTCACCTATGGATCAATTAGGATTTTCACCAT
CAGTTCAATCACACAGTCATAGTTTTAATCAGTCTTCAAGCTCCCAGTGGCGCCAAGGTACACCATCATCACAGCGTAAA
GTCAGAATGAATTCTCATCCCTACCTAGCAGATAGACATTATAGCCAGGAACAGCGTTGCACTGATCATGGGTCTGACCA
TCATTACAGAGGAAAGAGAGATGATTTCTTCTATGAAGATAGGAATCATGATGGCTGGAGCCATGACTATGATAACAGAA
GAGACAGTAGCAGAGATGGAAAATGGCGCTCATCTCGACAC

Alignment

ORF - retro_ptro_1617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.09 %
• Parental protein coverage: 95.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FVGNLETKVTEELLFELFHQAGPVIKVK-IPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPIK
          FVGNLETKVTEELLFELFHQAGPVIKVK.IPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPIK
Retrocopy FVGNLETKVTEELLFELFHQAGPVIKVK<IPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPIK

Parental  IQFRSGSSHAPQDVSLSYPQHHVGNSSPTSTSPSSRYERTMDNMTSSAQIIQRSFSSPENFQRQAVMNSA
          IQFRSGSSHA.QDVSL.YPQHHVGNSSPTSTSPS.RYERT.DNMTSSAQIIQRSFSSPENFQRQAVMNSA
Retrocopy IQFRSGSSHALQDVSLPYPQHHVGNSSPTSTSPS-RYERTRDNMTSSAQIIQRSFSSPENFQRQAVMNSA

Parental  LRQMSYGGKFGSSPLDQSGFSPSVQSHSHSFNQSSSSQWRQGTPSSQRKVRMNSYPYLADRHYSREQRYT
          LRQMSYGGKFGSSP.DQ.GFSPSVQSHSHSFNQSSSSQWRQGTPSSQRKVRMNS.PYLADRHYS.EQR.T
Retrocopy LRQMSYGGKFGSSPMDQLGFSPSVQSHSHSFNQSSSSQWRQGTPSSQRKVRMNSHPYLADRHYSQEQRCT

Parental  DHGSDHHYRGKRDDFFYEDRNHDGWSHDYDNRRDSSRDGKWRSSRH
          DHGSDHHYRGKRDDFFYEDRNHDGWSHDYDNRRDSSRDGKWRSSRH
Retrocopy DHGSDHHYRGKRDDFFYEDRNHDGWSHDYDNRRDSSRDGKWRSSRH

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	0.11 RPM	4.29 RPM
SRP007412_cerebellum	0.00 RPM	7.21 RPM
SRP007412_heart	0.03 RPM	9.21 RPM
SRP007412_kidney	0.05 RPM	12.47 RPM
SRP007412_liver	0.03 RPM	8.87 RPM
SRP007412_testis	0.00 RPM	18.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1617 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1617 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2283
Gorilla gorilla	retro_ggor_1696

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013514	1 retrocopy	retro_cfam_1021,
Choloepus hoffmanni	ENSCHOG00000012747	1 retrocopy	retro_chof_570,
Homo sapiens	ENSG00000076053	1 retrocopy	retro_hsap_2283,
Gorilla gorilla	ENSGGOG00000009941	1 retrocopy	retro_ggor_1696,
Loxodonta africana	ENSLAFG00000012444	1 retrocopy	retro_lafr_892,
Myotis lucifugus	ENSMLUG00000023234	2 retrocopies	retro_mluc_1555, retro_mluc_587,
Monodelphis domestica	ENSMODG00000013918	1 retrocopy	retro_mdom_535,
Mus musculus	ENSMUSG00000042396	1 retrocopy	retro_mmus_2436,
Nomascus leucogenys	ENSNLEG00000007323	1 retrocopy	retro_nleu_409,
Oryctolagus cuniculus	ENSOCUG00000003342	1 retrocopy	retro_ocun_924,
Otolemur garnettii	ENSOGAG00000016857	1 retrocopy	retro_ogar_3103,
Pongo abelii	ENSPPYG00000003894	1 retrocopy	retro_pabe_1669,
Pan troglodytes	ENSPTRG00000001243	1 retrocopy	retro_ptro_930,
Pan troglodytes	ENSPTRG00000004305	1 retrocopy	retro_ptro_1617 ,
Ictidomys tridecemlineatus	ENSSTOG00000012459	1 retrocopy	retro_itri_889,
Tursiops truncatus	ENSTTRG00000001515	3 retrocopies	retro_ttru_1316, retro_ttru_1441, retro_ttru_478,
Vicugna pacos	ENSVPAG00000006300	1 retrocopy	retro_vpac_311,