RetrogeneDB ID: retro_pabe_2548

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:114006644..114007684(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMX
• Ensembl ID: ENSPPYG00000020771
• Aliases: None
• Description: RNA binding motif protein, X-linked [Source:HGNC Symbol;Acc:9910]

Sequence

>retro_pabe_2548
GTTGAAGCAGATCGTCCAGGAAAGTTCTTCATTGGTGGACTTAATAAGGAAACAAATAAGAAAGCTCTTGAAGCAGTATT
TGGCAAATATGGACGAATAATGGAAGCACTCTTGATGAAAGACAGTGAAACCAACAAATCAAGAGGATTTGCTTTTGTCA
CCTTTGAAAACCCAGCAGACGCTAAGGATGCAGCCAGAGACATGAATGGAAAGTCATTAGATGAAAAGCCATCAAGGTGG
AACAAGCCACCAAACCATCATTTGAAAGGGTAGACGTGGACTGCCTCCACCTCCAAGAAGTAGAGGCCCTCCAAAAGGTC
TTAGAGGAGGAAGTGGAGGAAACAGGGGACCTCCCTCATGGAGAAGACACATGGATGATGGTGGATAGTCCATGAATTTT
AACATAAGTTCTTTCAGGGGACCACTCCCAGTAAAAAGAGGACCACCACCAAGAAGTGGGGGTCCTCCTCCTAAAAGATC
TGCACCTTCAGGACCAGTTCACAGCAGCTGTGGAATGGGAGGAAGAGCTCCTGTGTCACGTGGAAGAGATAGTTAGGGAG
GTCCACCTGGAAGGGAACAGCTGCCCTCTCATAGAGATGTTTATTTGCCCTCAAGAGATGATGGGTATTCTACAAAAGAC
AGCTCTTCAAGCAGAGATTACCCAAGTTCTCGTGATACAAGAGGTTATGCACCACCACCACGAGACTGTACTTACCGTGA
TTACGGTCATTTCAGTTCATGTGATGACTATCCATGAAGAGGCTATAGCGATAGAGATGGATATAGTCGTGATCATGACT
ATTCAGATCATCCAACTGGAGGTTCCTACAGAGATTCATATGAAAGTTATGGTAACTCACGTAGTGCTCCATCTACAGCA
GGCCCTCCCCCCATCTTATGGTGGAAGCGATGATTATAGCAGTTCACGTGACAGATATGGTGGAAGTCAAGACAGTTACT
CAAGCAGCCGAAGTCATCTCTAATCAAGTGGTCGTGGTCGGGTTGGCAGACAAGAAAGAGGGCTTCCCCCTTCTATGGAA

Alignment

ORF - retro_pabe_2548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.67 %
• Parental protein coverage: 90.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMNG
          VEADRPGK.FIGGLN.ETN.KALEAVFGKYGRI.E.LLMKD.ETNKSRGFAFVTFE.PADAKDAARDMNG
Retrocopy VEADRPGKFFIGGLNKETNKKALEAVFGKYGRIMEALLMKDSETNKSRGFAFVTFENPADAKDAARDMNG

Parental  KSLDGK-AIKVEQATKPSFE-SGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFN
          KSLD.K.AIKVEQATKPSFE..GRRG.PPPPRSRGPP.GL...RGGSGG.RGPPS...HMDDGG.SMNFN
Retrocopy KSLDEK<AIKVEQATKPSFE<KGRRGLPPPPRSRGPPKGL---RGGSGGNRGPPSWRRHMDDGG*SMNFN

Parental  MSSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSP
          .SS.RGPLPVKRGPPPRSGGPPPKRSAPSGPV.SS.GMGGRAPVSRGRDS.GGPP.RE.LPS.RDVYL..
Retrocopy ISSFRGPLPVKRGPPPRSGGPPPKRSAPSGPVHSSCGMGGRAPVSRGRDS*GGPPGREQLPSHRDVYLPS

Parental  RDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGG
          RDDGYSTKDS.SSRDYPSSRDTR.YAPPPRD.TYRDYGH.SS.DDYP.RGYSDRDGY.RD.DYSDHP.GG
Retrocopy RDDGYSTKDSSSSRDYPSSRDTRGYAPPPRDCTYRDYGHFSSCDDYP*RGYSDRDGYSRDHDYSDHPTGG

Parental  SYRDSYESYGNSRSAPPTRGP-PPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERG
          SYRDSYESYGNSRSAP.T.GP.PPSYGGS...DDYSSSRD.YGGS.DSYSSSRS.L.SSGR.RVGRQERG
Retrocopy SYRDSYESYGNSRSAPSTAGP>PPSYGGS---DDYSSSRDRYGGSQDSYSSSRSHL*SSGRGRVGRQERG

Parental  LPPSME
          LPPSME
Retrocopy LPPSME

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	25.27 RPM
SRP007412_cerebellum	0.73 RPM	34.53 RPM
SRP007412_heart	0.00 RPM	28.21 RPM
SRP007412_kidney	0.03 RPM	34.37 RPM
SRP007412_liver	0.00 RPM	19.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2548 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2548 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2548 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3074

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013308	1 retrocopy	retro_btau_36,
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778,
Dasypus novemcinctus	ENSDNOG00000017199	3 retrocopies	retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
Dipodomys ordii	ENSDORG00000015481	1 retrocopy	retro_dord_793,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Monodelphis domestica	ENSMODG00000014054	1 retrocopy	retro_mdom_1231,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Otolemur garnettii	ENSOGAG00000007839	5 retrocopies	retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Ochotona princeps	ENSOPRG00000016593	1 retrocopy	retro_opri_372,
Pongo abelii	ENSPPYG00000017728	1 retrocopy	retro_pabe_324,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548 , retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Sorex araneus	ENSSARG00000000397	1 retrocopy	retro_sara_169,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tarsius syrichta	ENSTSYG00000009555	1 retrocopy	retro_tsyr_15,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,