RetrogeneDB ID: retro_ptro_2898

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:74883691..74884438(-)
• Located in intron of: ENSPTRG00000021033

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_2898
GAAGAGTACTACACGCAGAATGTGGAGAGAGGGATTTCTAACTCGAATGGAAGACAGCCAGTTGGCCTGCTGGGGAAAGC
TACATCCACCAGTGACATGCTAGACAAACTGGCCTGGACCATACCCTATTACCTAAAGAATAAGCCCCACATTTGCTCCT
TCTGGGTGAAGGGAGAGGGTAAGAGAGGAGAGGAGTTTCGATAGAGACATGAGAAGCCTACAGGTCCACATGATTCCCTT
GCTGATCGGATATTAAAAACTGATATTATATAGTCAATGACCCTGTAGCAGATAAGCTTCTATAGTAGGCTTCAGCCACG
CCTCATCTGGAACTCCCAGAGGATAAGACTATCCCCACACTAGACACTGGTGATCCGGGTGATACCATTACTGAGACAGA
TCTTAAGAAATAATCTCTACCTATTTAGAGAGATCTGGACAATCCCTGTTGTGCAGAGACAACGGTGTGCTTTCATCCAG
GTTTCCACAGGGCAGGCTGCACAAGTGGCTGCAGAGAAGTCCTTTAATAAGTTAATCACCAATGGCTGCAGACTAAGTGT
AAAATGGGGAAGATCCCAGGCAGCCAGAGGAAAGGAAAATGACAGAACCCCAGACCCGGGGATCCAGCTAGAGCTGATTC
CAGTACTGCCGGGAGCTCTTCCTCCTTCTGCAGCAGCAGATGCATCTGCCAATGACTTCAACCTACCTCCAAGTGCTCCT
ACAGCTGCGGTGAACATTGCCTTGCCG

Alignment

ORF - retro_ptro_2898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.37 %
• Parental protein coverage: 60.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECPYRH
          .EYYTQN.ER.ISNS.G..PVG.LGKATSTSDML.KLA.T.PYY..N.PHICSFWVKGE.KRGEE...RH
Retrocopy EEYYTQNVERGISNSNGRQPVGLLGKATSTSDMLDKLAWTIPYYLKNKPHICSFWVKGEGKRGEEFR*RH

Parental  EKPTDPDDPLADQ-NIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLGDTITETD-LRNH
          EKPT.P.D.LAD...IK..YY..NDPVADKLL..AS..P.L..PEDKTI.TL..G..GDTITETD.LRN.
Retrocopy EKPTGPHDSLADR<DIKN*YYIVNDPVADKLL**ASATPHLELPEDKTIPTLDTGDPGDTITETD>LRNN

Parental  FYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGTTDS
          .Y.F.EI.TI.VVQRQ.CAFIQ..T.QAA.VAAEKSFNKLI.NG.RL.VKWGRSQAARG..KE.D.T.D.
Retrocopy LYLFREIWTIPVVQRQRCAFIQVSTGQAAQVAAEKSFNKLITNGCRLSVKWGRSQAARG--KENDRTPDP

Parental  GIKLEPVPGLPGALPPPPAAEEEASANYFNLPPSGPPAVVNIALP
          GI.LE..P.LPGALPP..AA...ASAN.FNLPPS.P.A.VNIALP
Retrocopy GIQLELIPVLPGALPPSAAA--DASANDFNLPPSAPTAAVNIALP

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	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_2898 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2898 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2898 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4273
Gorilla gorilla	retro_ggor_2859
Pongo abelii	retro_pabe_3486
Macaca mulatta	retro_mmul_1199

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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,