RetrogeneDB ID: retro_ptro_2348

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:45754876..45755535(+)
• Located in intron of: ENSPTRG00000023379

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSPTRG00000017423
• Aliases: None
• Description: None

Sequence

>retro_ptro_2348
CAATCAGAATATTATGGAATCAATGATCCAGAAACAGATAAGCATCTAAAGTGGGCTTCAATCATGCCCCATCTGGACCC
ATCAGAGGACAAGGTTATCCTCCCCATATGTTGGTAGTCTGGATAATACCATTTCTGAGACAGATCTAAGACATCATCAC
TACCAGTTTGGAGAGATGCAGATTGATTACTGTTGTTCAGAGAGAGCAGTGTGCTTTCATCCAGGTTTCCACAGGGCAGG
CTGCAGAAGTGGCTGCTGAGAAGTCCTTTGATAAGTTGATTGTCAATGGCTGTAGACTCAACATAAAATGGGGAAGATCC
CAAGCATCCAGAGGAAAAGAAAAAGAGAAGAACAGATCACAGACTCTGGGATCCAGCTACAGCCTATTCCAGCACTGCCA
TGAGCTCTTCCTCCTCCTACAGCAGCAGCAGATGCATGTACCAACTACTTCAACCTGCCCCAACATGGTCCTCCAGCTGT
GGTGAACATTGCCCAGCCACCAGCCCCTAGTCTTCCACACCCCCAACCCCAGGATTTAGGCCACACATATTCACCTCAAT
GGGACCACCCTTTCCTTTCATGACAACTCCAGGATTAATCCACTATCTTTCTCATGACCTCAGAGGATGGGAGCTCATGC
CAGAAAACATAGGAAACCC

Alignment

ORF - retro_ptro_2348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.96 %
• Parental protein coverage: 52.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KDRYYGINDPVADKLLKRASTMPRLDPPEDKTI-TTLYVGGLGDTITETDLRNHFYQFGEI-RTITVVQR
          ...YYGINDP..DK.LK.AS.MP.LD.P.........YVG.L..TI.ETDLR.H.YQFGE..R.ITVVQR
Retrocopy QSEYYGINDPETDKHLKWASIMPHLD-PSEDKV>SSPYVGSLDNTISETDLRHHHYQFGEM>RLITVVQR

Parental  QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGT-TDSGIKLEPVPGLPGAL
          .QCAFIQ..T.QAAEVAAEKSF.KLIVNG.RLN.KWGRSQA.RGKEKEK....TDSGI.L.P.P.LP.AL
Retrocopy EQCAFIQVSTGQAAEVAAEKSFDKLIVNGCRLNIKWGRSQASRGKEKEKNRS<TDSGIQLQPIPALP*AL

Parental  PPPPAAEEEASANYFNLPPSGPPAVVNIALPPPPGI-APPPPPGFGPHMFHPMGPPPPFMRAPGPIHYPS
          PPP.AA...A..NYFNLP..GPPAVVNIA.PP.P.....PP.PGF.PH.F..MGPP.PFM..PG.IHY.S
Retrocopy PPPTAA-ADACTNYFNLPQHGPPAVVNIAQPPAPSL<STPPTPGFRPHIFTSMGPPFPFMTTPGLIHYLS

Parental  QD-PQRMGAHAGKHSSP
          .D.PQRMGAHA.KH..P
Retrocopy HD<PQRMGAHARKHRKP

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	0.04 RPM	24.61 RPM
SRP007412_cerebellum	0.00 RPM	42.77 RPM
SRP007412_heart	0.00 RPM	15.16 RPM
SRP007412_kidney	0.00 RPM	32.25 RPM
SRP007412_liver	0.00 RPM	19.18 RPM
SRP007412_testis	0.00 RPM	24.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2348 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2348 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3465
Gorilla gorilla	retro_ggor_2337
Pongo abelii	retro_pabe_2861
Macaca mulatta	retro_mmul_1762

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018082	1 retrocopy	retro_cfam_1480,
Callithrix jacchus	ENSCJAG00000020963	6 retrocopies	retro_cjac_1338, retro_cjac_2471, retro_cjac_3342, retro_cjac_3390, retro_cjac_3934, retro_cjac_990,
Cavia porcellus	ENSCPOG00000001946	2 retrocopies	retro_cpor_280, retro_cpor_283,
Dasypus novemcinctus	ENSDNOG00000011166	1 retrocopy	retro_dnov_2298,
Homo sapiens	ENSG00000086589	2 retrocopies	retro_hsap_3465, retro_hsap_4273,
Gorilla gorilla	ENSGGOG00000012947	2 retrocopies	retro_ggor_2337, retro_ggor_2859,
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Macaca mulatta	ENSMMUG00000020683	4 retrocopies	retro_mmul_1199, retro_mmul_1348, retro_mmul_1553, retro_mmul_1762,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186,
Pongo abelii	ENSPPYG00000015955	4 retrocopies	retro_pabe_1412, retro_pabe_1594, retro_pabe_2861, retro_pabe_3486,
Pan troglodytes	ENSPTRG00000017423	2 retrocopies	retro_ptro_2348 , retro_ptro_2898,
Tarsius syrichta	ENSTSYG00000003939	3 retrocopies	retro_tsyr_1090, retro_tsyr_1187, retro_tsyr_1231,