RetrogeneDB ID: retro_hsap_3465

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:45066339..45066999(+)
• Located in intron of: ENSG00000196284

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSG00000086589
• Aliases: RBM22, Cwc2, ZC3H16, fSAP47
• Description: RNA binding motif protein 22 [Source:HGNC Symbol;Acc:25503]

Sequence

>retro_hsap_3465
CAATCAGAATATTATGGAATCAATGATCCAGAAACAGATAAGCATCTAAAGTGGGCTTCAATCATGCCCCATCTGGACCC
ATCAGAGGACAAGGTTATCCTCCCCATATGTTGGTAGTCTGGATAATACCCTTTCTGAGACAGATCTAAGACATCATCAC
TACCAGTTTGGAGAGATGCAGATTGATTACTGTTGTTCAGAGAGAGCAGTGTGCTTTCATCCAGGTTTCCACAGGGCAGG
CTGCAGAAGTGGCTGCTGAGAAGTCCTTTGATAAGTTGATTGTCAATGGCTGTAGACTCAACATAAAATGGGGAAGATCC
CAAGCATCCAGAGGAAAAGAAAAAGAGAAGAACAGATCACAGACTCTGGGATCCAGCTACAGCCTATTCCAGCACTGCCA
TGAGCTCTTCCTCCTCCTACAGCAGCAGAAGATGCATGTGCCAGCTACTTCAACCTGCCCCAACATGGTCCTCCAGCTGT
GGTGAACATTGCCCAGCCACCAGCCCCTAGTCTTCCACACCCCCAACCCCAGGATTTAGGCCACACATATTCACCTCAAT
GGGACCACCCTTTCCTTTCATGACAACTCCAGGATTAATCCACTATCTTTCTCATGACCCTCAGAGGATGGGAGCTCATG
CCAGAAAACATAGGAAACCC

Alignment

ORF - retro_hsap_3465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.26 %
• Parental protein coverage: 59.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KDRYYGINDPVADKLLKRASTMPRLDPPEDKTI-TTLYVGGLGDTITETDLRNHFYQFGEI-RTITVVQR
          ...YYGINDP..DK.LK.AS.MP.LD.P.........YVG.L..T..ETDLR.H.YQFGE..R.ITVVQR
Retrocopy QSEYYGINDPETDKHLKWASIMPHLD-PSEDKV>SSPYVGSLDNTLSETDLRHHHYQFGEM>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.E.A.A.YFNLP..GPPAVVNIA.PP.P.....PP.PGF.PH.F..MGPP.PFM..PG.IHY.S
Retrocopy PPPTAA-EDACASYFNLPQHGPPAVVNIAQPPAPSL<STPPTPGFRPHIFTSMGPPFPFMTTPGLIHYLS

Parental  QDPQRMGAHAGKHSSP
          .DPQRMGAHA.KH..P
Retrocopy HDPQRMGAHARKHRKP

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
bodymap2_adipose	0.08 RPM	37.31 RPM
bodymap2_adrenal	0.00 RPM	42.06 RPM
bodymap2_brain	0.00 RPM	34.22 RPM
bodymap2_breast	0.00 RPM	35.45 RPM
bodymap2_colon	0.00 RPM	38.03 RPM
bodymap2_heart	0.02 RPM	23.81 RPM
bodymap2_kidney	0.00 RPM	38.24 RPM
bodymap2_liver	0.00 RPM	15.00 RPM
bodymap2_lung	0.00 RPM	52.25 RPM
bodymap2_lymph_node	0.00 RPM	47.26 RPM
bodymap2_ovary	0.02 RPM	63.96 RPM
bodymap2_prostate	0.00 RPM	48.83 RPM
bodymap2_skeletal_muscle	0.00 RPM	49.98 RPM
bodymap2_testis	0.00 RPM	44.32 RPM
bodymap2_thyroid	0.06 RPM	39.51 RPM
bodymap2_white_blood_cells	0.00 RPM	80.90 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3465 was not detected

EST

No EST(s) were mapped for retro_hsap_3465 retrocopy.

TSS

No TSS is located nearby retro_hsap_3465 retrocopy 5' end.

Lab

retro_hsap_3465 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3465 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2348
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).