RetrogeneDB ID: retro_pabe_2861

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:45068697..45069340(+)
• Located in intron of: ENSPPYG00000016663

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSPPYG00000015955
• Aliases: None
• Description: pre-mRNA-splicing factor RBM22 [Source:RefSeq peptide;Acc:NP_001125624]

Sequence

>retro_pabe_2861
CAATCAGAATATTATGGAATCAATGATCCAGAAACAGATAAGCATCTAAAGTGGGCTTCAATCATGCTCCATCTGGACCC
ATCAGAGGACAAGGTTATCCTCCCTATATGTTGGTAGTCTGGGTAATACCATTTCTGAGACAGATCTAAGACATCATCAC
TACCAGTTTGGAGAGATGCAGATGATTACTGTTGTTCAGAGAGAGCAGTGTGCTTTCATCCAGGTTTCCACAGGGCAGGC
TGCAGAAGTGGCTGCTGAGAAGTCCTTTGATAAGTTGATTGTCAATGGCTGTAGACTCAACATAAAATGGGGAAGATCCC
AAGCATCCAGAGGAAAAGAAAAAGAGAAGAACAGATCACAGACTCTGGGATCCAGCTACAGCCTATTCCAGCACTGCCAT
GAGCTCTTCCTCCTCCTACAGCAGCAGAAGATGCATGCTACTTCGACCGCCCCAACATGGTCCTCCAGCTGTGGTGAACA
TTGCCCAGCCACCAGCCCCTAGTTTTCCACACCCCCAACCCCAGGATTTAGGCCACACATATTCACCTCAATGGGACCAC
CCCTTCCTTTCATGACGACTCCAGGATTAATCCACTATCTTTCTCATGACCCTCAGAGGATGGGAGCTCATGCCAGAAAT
CAT

Alignment

ORF - retro_pabe_2861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.37 %
• Parental protein coverage: 52.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KDRYYGINDPVADKLLKRASTMPRLDPPEDKTI-TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ
          ...YYGINDP..DK.LK.AS.M..LD.P........LYVG.LG.TI.ETDLR.H.YQFGE...ITVVQR.
Retrocopy QSEYYGINDPETDKHLKWASIMLHLD-PSEDKV>SSLYVGSLGNTISETDLRHHHYQFGEMQMITVVQRE

Parental  QCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGT-TDSGIKLEPVPGLPGALP
          QCAFIQ..T.QAAEVAAEKSF.KLIVNG.RLN.KWGRSQA.RGKEKEK....TDSGI.L.P.P.LP.ALP
Retrocopy QCAFIQVSTGQAAEVAAEKSFDKLIVNGCRLNIKWGRSQASRGKEKEKNRS<TDSGIQLQPIPALP*ALP

Parental  PPPAAEEEASANYFNL-PPSGPPAVVNIALPPPPG-IAPPPPPGFGPHMFHPMGPPPPFMRAPGPIHYPS
          PP.AAE....A.YF...P..GPPAVVNIA.PP.P.....PP.PGF.PH.F..MGPP.PFM..PG.IHY.S
Retrocopy PPTAAED---ACYFDR<PQHGPPAVVNIAQPPAPS<FSTPPTPGFRPHIFTSMGPPLPFMTTPGLIHYLS

Parental  QDPQRMGAHAGKH
          .DPQRMGAHA..H
Retrocopy HDPQRMGAHARNH

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	21.73 RPM
SRP007412_cerebellum	0.00 RPM	21.77 RPM
SRP007412_heart	0.00 RPM	9.06 RPM
SRP007412_kidney	0.00 RPM	26.38 RPM
SRP007412_liver	0.03 RPM	16.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2861 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2861 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3465
Pan troglodytes	retro_ptro_2348
Gorilla gorilla	retro_ggor_2337
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,