RetrogeneDB ID: retro_pabe_1601

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:63622655..63623285(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF10
• Ensembl ID: ENSPPYG00000001726
• Aliases: SRSF10, FUSIP1, SFRS13A
• Description: splicing factor, arginine/serine-rich 13A [Source:RefSeq peptide;Acc:NP_001125358]

Sequence

>retro_pabe_1601
ATGTCCCACTACCTGCACACTCCTCCAAAACATGTCTCTGTCCATCAGGAACATGGCCAGTGACACCAGGTCTGCAGATG
GACAGGATAAATTTGGTCATGATGGTCCTACAGGAGTTGTTTATGTTCCACTTGATTTCCACACCCGCCGTCCAAGAGGA
TTTGCTTATGTTCAATTTGAGGATGTTTGTGATGCTGAAGATGCTTTTGCATAATTTGGACAGGAAATAGATTTGTGGAC
ATCAAGCTGAAATACAGTTTACACAGGGGGATGAGAAGACACCAAATTCAGATGAAATCCAAGGAACAGAGGAATGTGTA
CAGCTCTTCGCGCCATGATGGTTTATGACAGAATACACAAGTTCTAGAAGACCAAAGTTTATGAAAAGGAGATCCAGAAG
TCAGTCTTTTGATTACAGTTATAGAAAGATCTTACAGTCCTAGAAATCAACCGACTGGAAAACCACGGAGTAGCAGAAGC
CATTCCGACAATGGTGGATTCAAACACCAAAATCCATCTTTTTCAAGATCTACATCTCATTCAAGGCAGCCCAAGGAAGA
AGTGAAGGCTAAATCACATTCTAGGTCTGCATCTCACACCAAAACCAGAGGCACCTCTAAAACAGATTCC

Alignment

ORF - retro_pabe_1601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 81.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MSRYLR-PP-NTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDA-
          MS.YL..PP.N.SL..RN.A.DTRS.D....FG..GP...VYVPLDF.TRRPRGFAYVQFEDV.DAEDA.
Retrocopy MSHYLHTPP>NMSLSIRNMASDTRSADGQDKFGHDGPTGVVYVPLDFHTRRPRGFAYVQFEDVCDAEDA>

Parental  LHNLDRKWICGRQIEIQFAQGDRKTPN-QMKAKEGRNVYSSSRYDD-YDR-YRRSRSRSYERRRSRSRSF
          LHNLDRK.ICG.Q.EIQF.QGD.KTPN.QMK.KE.RNVYSSSR.D..YDR.Y..SR......RRSRS.SF
Retrocopy LHNLDRK*ICGHQAEIQFTQGDEKTPN>QMKSKEQRNVYSSSRHDG>YDR>YTSSRRPKFMKRRSRSQSF

Parental  DYNYR-RSYSPRNSRPTGRPRRSRSHSDNDRFKHRNRSFSRSKSNSRSRSKSQPKKEMKAKSRSRSASHT
          DY.YR.RSYSPRN..PTG.PR.SRSHSDN..FKH.N.SFSRS.S.SR...........K..SRS..ASHT
Retrocopy DYSYR>RSYSPRN-QPTGKPRSSRSHSDNGGFKHQNPSFSRSTSHSR---QPKEEVKAKSHSRS--ASHT

Parental  KTRGTSKTDS
          KTRGTSKTDS
Retrocopy KTRGTSKTDS

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	0.06 RPM	25.71 RPM
SRP007412_cerebellum	0.00 RPM	40.49 RPM
SRP007412_heart	0.03 RPM	18.94 RPM
SRP007412_kidney	0.03 RPM	26.19 RPM
SRP007412_liver	0.03 RPM	20.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1601 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1601 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1940
Pan troglodytes	retro_ptro_1295
Gorilla gorilla	retro_ggor_1411
Callithrix jacchus	retro_cjac_1170

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009869	2 retrocopies	retro_amel_1810, retro_amel_355,
Bos taurus	ENSBTAG00000008072	1 retrocopy	retro_btau_759,
Choloepus hoffmanni	ENSCHOG00000004836	1 retrocopy	retro_chof_7,
Callithrix jacchus	ENSCJAG00000020883	9 retrocopies	retro_cjac_1126, retro_cjac_1170, retro_cjac_2176, retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus	ENSCPOG00000024533	1 retrocopy	retro_cpor_1098,
Dasypus novemcinctus	ENSDNOG00000008699	3 retrocopies	retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Erinaceus europaeus	ENSEEUG00000014286	1 retrocopy	retro_eeur_522,
Homo sapiens	ENSG00000188529	5 retrocopies	retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054, retro_hsap_4295,
Gorilla gorilla	ENSGGOG00000000392	4 retrocopies	retro_ggor_1044, retro_ggor_1411, retro_ggor_1522, retro_ggor_2870,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Mustela putorius furo	ENSMPUG00000015845	1 retrocopy	retro_mputfur_353,
Nomascus leucogenys	ENSNLEG00000013180	3 retrocopies	retro_nleu_1647, retro_nleu_1825, retro_nleu_202,
Oryctolagus cuniculus	ENSOCUG00000029326	1 retrocopy	retro_ocun_717,
Otolemur garnettii	ENSOGAG00000015374	2 retrocopies	retro_ogar_2650, retro_ogar_2987,
Pongo abelii	ENSPPYG00000001726	4 retrocopies	retro_pabe_1115, retro_pabe_1601 , retro_pabe_1796, retro_pabe_2529,
Rattus norvegicus	ENSRNOG00000007992	3 retrocopies	retro_rnor_1657, retro_rnor_2800, retro_rnor_2829,
Sus scrofa	ENSSSCG00000021615	2 retrocopies	retro_sscr_528, retro_sscr_554,
Ictidomys tridecemlineatus	ENSSTOG00000000956	1 retrocopy	retro_itri_1333,
Tursiops truncatus	ENSTTRG00000016150	2 retrocopies	retro_ttru_1098, retro_ttru_695,