RetrogeneDB ID: retro_sscr_851

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:120077925..120078386(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBPMS2
• Ensembl ID: ENSSSCG00000004549
• Aliases: None
• Description: RNA binding protein with multiple splicing 2 [Source:HGNC Symbol;Acc:19098]

Sequence

>retro_sscr_851
CAGGGGTATGAAGCGTCCCTCATCAAGCTCACATTGAGACAGCCTGTCAGCTTTACTATCTTTGACAGCCAGGCCGCAGC
CTAAGTGGCCAAAAATTCATGGAAAGTTATGTGCTTTGATCTGAAGAATTTGCAGACTTTTGAGGCTAGAGTTTGCCAAA
GCCAAACCAAGATGGCCAAGAACAAGCTAATGCCAACATCAAATCCCAATGTTCAGTGTGCCCTAGGAGCACATCTCATC
ACAAGGGACCCCTATGAGGTTGCTCTCATCCCCGAGTCCCCAGAGGCCTGGGCCCCCTACCCTTGTGTACCCCAGAGACC
TGACCCCAGCATCTCACCTGCTGCCTTCACCTACCTACCCAGCTGCCACTGCTGTTGCTGTCTCTGTCCCCCCTGCTCTA
CTGAGGCTGGTACACTTCCCCCCATACCACCCAGCAAGGATGAAACTGTCCTCAATTCTGT

Alignment

ORF - retro_sscr_851 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.25 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KGYEGSLIKLTSRQPVGFVIFDSRAGAEAAKNALNGIRFDPENPQT-LRLEFAKAN-TKMAKNKLMATPN
          .GYE.SLIKLT.RQPV.F.IFDS.A.A..AKN......FD..N.QT.LRLEFAKA..TKMAKNKLM.T.N
Retrocopy QGYEASLIKLTLRQPVSFTIFDSQAAA*VAKNSWKVMCFDLKNLQT>LRLEFAKAK<TKMAKNKLMPTSN

Parental  PTNTHPALGAHFIARDPYDLMGAALIPASPEAWAPYPLYTTELTPVISHAAFTY-PA-ATAAAAATLHTQ
          P.N...ALGAH.I.RDPY.....ALIP.SPEAWAPYP.......P.IS.AAFTY.P..ATA.A.......
Retrocopy P-NVQCALGAHLITRDPYEV---ALIPESPEAWAPYPCVPQRPDPSISPAAFTYLPS>ATAVAVSVPPAL

Parental  VR-WYPSSDTTQQGWKYRQFC
          .R.WY.S..TTQQG....QFC
Retrocopy LR>WYTSPHTTQQG*NCPQFC

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
SRP014902_placenta	0.00 RPM	0.66 RPM
SRP014902_testis	0.00 RPM	9.19 RPM
SRP018288_heart	0.00 RPM	49.03 RPM
SRP018288_kidney	0.00 RPM	28.47 RPM
SRP018288_liver	0.00 RPM	6.56 RPM
SRP018288_lung	0.00 RPM	11.20 RPM
SRP018856_adipose	0.00 RPM	19.20 RPM
SRP035408_brain	0.00 RPM	2.16 RPM
SRP035408_liver	0.00 RPM	7.16 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_851 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_851 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_851 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011037	1 retrocopy	retro_btau_1674,
Callithrix jacchus	ENSCJAG00000005200	2 retrocopies	retro_cjac_1775, retro_cjac_298,
Dipodomys ordii	ENSDORG00000004025	1 retrocopy	retro_dord_438,
Homo sapiens	ENSG00000166831	2 retrocopies	retro_hsap_2513, retro_hsap_3613,
Gorilla gorilla	ENSGGOG00000008984	1 retrocopy	retro_ggor_2438,
Loxodonta africana	ENSLAFG00000018725	6 retrocopies	retro_lafr_344, retro_lafr_393, retro_lafr_445, retro_lafr_481, retro_lafr_550, retro_lafr_859,
Macaca mulatta	ENSMMUG00000013270	1 retrocopy	retro_mmul_1837,
Monodelphis domestica	ENSMODG00000010487	1 retrocopy	retro_mdom_571,
Mus musculus	ENSMUSG00000032387	9 retrocopies	retro_mmus_2671, retro_mmus_3408, retro_mmus_3410, retro_mmus_3429, retro_mmus_3431, retro_mmus_3437, retro_mmus_3562, retro_mmus_3588, retro_mmus_3596,
Nomascus leucogenys	ENSNLEG00000012505	1 retrocopy	retro_nleu_2209,
Otolemur garnettii	ENSOGAG00000026017	1 retrocopy	retro_ogar_3254,
Pongo abelii	ENSPPYG00000006553	1 retrocopy	retro_pabe_2963,
Pan troglodytes	ENSPTRG00000007165	2 retrocopies	retro_ptro_1458, retro_ptro_2441,
Sus scrofa	ENSSSCG00000004549	1 retrocopy	retro_sscr_851 ,
Ictidomys tridecemlineatus	ENSSTOG00000010055	2 retrocopies	retro_itri_1512, retro_itri_556,
Tarsius syrichta	ENSTSYG00000008996	3 retrocopies	retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tursiops truncatus	ENSTTRG00000011840	3 retrocopies	retro_ttru_1046, retro_ttru_1212, retro_ttru_1790,