RetrogeneDB ID: retro_sscr_431

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:35247874..35248310(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000030632
• Aliases: None
• Description: Sus scrofa ubiquitin-conjugating enzyme E2 variant 1 (UBE2V1), mRNA. [Source:RefSeq mRNA;Acc:NM_001205094]

Sequence

>retro_sscr_431
ATGGCAGCCACCACAGGCTGGGGAGTAAAAGTCCCTCGCAATTTCCAACTGTTGGAAGAACTTGAAGAAGGCCAGAAAGC
AGTAGGAGATGCAGTTAGCTGGGGTCTACAAGATGTTGAAGACATGACACTTACAAGATGACAAGAATGATAATTGGGCC
TCCAAGAACAACTTATGAAAACTGAATATACAGCCTTAAAATAGACTGTGGACCTAAATACCCAGAAGTGCCCCCCCTGT
AAGATTTGTAATAGAAATTAATATGAATGAAGTTAATAGTTCTAATGGAGGGGTGGACCCCAGAGCCATATCAGTGCTAG
CAAAATGGAAGAATTCACATAGCATCAAAGTTGTTCTGCAAGAGCTTTGATACCTAATGAGGTCTAAAGAACATATGCAA
CACCCTCAGCCACCTGAAGGACAGTGTTACAGCAAT

Alignment

ORF - retro_sscr_431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAATTGSGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTR-WTGMIIGPPRTIYENRIYSLKI
          MAATTG.GVKVPRNF.LLEELEEGQK.VGD..VSWGL.D.EDMTLTR..T.MIIGPPRT.YEN.IYSLKI
Retrocopy MAATTGWGVKVPRNFQLLEELEEGQKAVGDA-VSWGLQDVEDMTLTR<MTRMIIGPPRTTYEN*IYSLKI

Parental  ECGPKYPEAPPF-VRFVTKINMNGVNSSNGVVDPRAISVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQ
          .CGPKYPE.PP..VRFV..INMN.VNSSNG.VDPRAISVLAKW.NS.SIKVVLQEL..LM.SKE.M..PQ
Retrocopy DCGPKYPEVPPL<VRFVIEINMNEVNSSNGGVDPRAISVLAKWKNSHSIKVVLQEL*YLMRSKEHMQHPQ

Parental  PPEGQCYSN
          PPEGQCYSN
Retrocopy PPEGQCYSN

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	34.64 RPM
SRP014902_testis	0.00 RPM	39.89 RPM
SRP018288_heart	0.00 RPM	59.30 RPM
SRP018288_kidney	0.00 RPM	94.27 RPM
SRP018288_liver	0.00 RPM	60.29 RPM
SRP018288_lung	0.00 RPM	135.23 RPM
SRP018856_adipose	0.17 RPM	79.71 RPM
SRP035408_brain	0.00 RPM	122.25 RPM
SRP035408_liver	0.00 RPM	52.37 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_431 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_431 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_431 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027316	4 retrocopies	retro_btau_1196, retro_btau_1226, retro_btau_1307, retro_btau_415,
Callithrix jacchus	ENSCJAG00000036984	10 retrocopies	retro_cjac_1076, retro_cjac_1952, retro_cjac_2810, retro_cjac_2865, retro_cjac_3081, retro_cjac_3140, retro_cjac_3258, retro_cjac_4089, retro_cjac_462, retro_cjac_974,
Homo sapiens	ENSG00000244687	4 retrocopies	retro_hsap_2175, retro_hsap_2440, retro_hsap_2884, retro_hsap_4192,
Loxodonta africana	ENSLAFG00000027359	2 retrocopies	retro_lafr_1026, retro_lafr_1221,
Macaca mulatta	ENSMMUG00000012228	6 retrocopies	retro_mmul_1722, retro_mmul_2382, retro_mmul_351, retro_mmul_436, retro_mmul_629, retro_mmul_907,
Mustela putorius furo	ENSMPUG00000017557	3 retrocopies	retro_mputfur_1522, retro_mputfur_384, retro_mputfur_834,
Nomascus leucogenys	ENSNLEG00000006987	8 retrocopies	retro_nleu_1554, retro_nleu_1612, retro_nleu_1996, retro_nleu_2206, retro_nleu_2773, retro_nleu_3025, retro_nleu_304, retro_nleu_566,
Oryctolagus cuniculus	ENSOCUG00000026172	4 retrocopies	retro_ocun_1450, retro_ocun_1481, retro_ocun_454, retro_ocun_539,
Otolemur garnettii	ENSOGAG00000025894	12 retrocopies	retro_ogar_1381, retro_ogar_1391, retro_ogar_153, retro_ogar_1637, retro_ogar_1929, retro_ogar_2027, retro_ogar_2478, retro_ogar_2984, retro_ogar_3172, retro_ogar_3338, retro_ogar_620, retro_ogar_80,
Pan troglodytes	ENSPTRG00000013615	1 retrocopy	retro_ptro_64,
Rattus norvegicus	ENSRNOG00000025580	21 retrocopies	retro_rnor_1014, retro_rnor_1032, retro_rnor_1291, retro_rnor_1609, retro_rnor_1649, retro_rnor_1650, retro_rnor_1651, retro_rnor_2055, retro_rnor_2282, retro_rnor_2406, retro_rnor_2407, retro_rnor_2412, retro_rnor_2488, retro_rnor_2489, retro_rnor_2490, retro_rnor_2534, retro_rnor_2535, retro_rnor_2905, retro_rnor_819, retro_rnor_881, retro_rnor_991,
Sus scrofa	ENSSSCG00000022190	1 retrocopy	retro_sscr_524,
Sus scrofa	ENSSSCG00000030632	1 retrocopy	retro_sscr_431 ,
Ictidomys tridecemlineatus	ENSSTOG00000014322	6 retrocopies	retro_itri_1001, retro_itri_1002, retro_itri_1134, retro_itri_1452, retro_itri_1600, retro_itri_992,