RetrogeneDB ID: retro_sscr_249

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:63578468..63578728(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO2
• Ensembl ID: ENSSSCG00000017212
• Aliases: SUMO2, PSMT3, SMT3H2, Smt3A
• Description: Sus scrofa SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae) (SUMO2), mRNA. [Source:RefSeq mRNA;Acc:NM_213984]

Sequence

>retro_sscr_249
GAGCCCAAAGAAGCAGTCGGGGCTGAGAACGACAATCATATTAACGTGAGGGTGGCGGGGCAGGATGGTTCTGCGGCATT
TAAGATCAAGAGACATACACCACTTAGGACACTAATGAAAGCCTATTGTGAATGACAGGGTTTGTCAATGAGGCAGATCA
GATTCTGACTTGATGGGCAGCCAGTCGATGAAACAGACACACCTGCCCAGTGGAACTGGAGGATGAAGATACAGCTGATG
TGCTCCAGCGGCCGACAGGA

Alignment

ORF - retro_sscr_249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.91 %
• Parental protein coverage: 92.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPA
          .PKE.V..EN..HIN..VAGQDGS...FKIKRHTPL..LMKAYCE.QGLSMRQIRF..DGQP..ETDTPA
Retrocopy EPKEAVGAENDNHINVRVAGQDGSAA-FKIKRHTPLRTLMKAYCE*QGLSMRQIRF*LDGQPVDETDTPA

Parental  Q-LEMEDEDTIDVFQQQTG
          Q..E.EDEDT.DV.Q..TG
Retrocopy Q<VELEDEDTADVLQRPTG

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	0.53 RPM	46.46 RPM
SRP014902_testis	0.85 RPM	114.15 RPM
SRP018288_heart	0.05 RPM	81.17 RPM
SRP018288_kidney	0.10 RPM	121.56 RPM
SRP018288_liver	0.00 RPM	50.53 RPM
SRP018288_lung	0.20 RPM	85.33 RPM
SRP018856_adipose	0.18 RPM	126.23 RPM
SRP035408_brain	0.00 RPM	115.29 RPM
SRP035408_liver	0.00 RPM	37.28 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_249 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_249 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009189	13 retrocopies	retro_amel_1097, retro_amel_1125, retro_amel_1199, retro_amel_1263, retro_amel_1434, retro_amel_152, retro_amel_1665, retro_amel_276, retro_amel_35, retro_amel_616, retro_amel_653, retro_amel_662, retro_amel_722,
Cavia porcellus	ENSCPOG00000004581	9 retrocopies	retro_cpor_1029, retro_cpor_1297, retro_cpor_1496, retro_cpor_202, retro_cpor_357, retro_cpor_823, retro_cpor_838, retro_cpor_869, retro_cpor_894,
Homo sapiens	ENSG00000188612	2 retrocopies	retro_hsap_4036, retro_hsap_4095,
Loxodonta africana	ENSLAFG00000025811	10 retrocopies	retro_lafr_104, retro_lafr_1222, retro_lafr_1240, retro_lafr_200, retro_lafr_254, retro_lafr_324, retro_lafr_36, retro_lafr_488, retro_lafr_858, retro_lafr_888,
Monodelphis domestica	ENSMODG00000007222	11 retrocopies	retro_mdom_1263, retro_mdom_1472, retro_mdom_1474, retro_mdom_1560, retro_mdom_1598, retro_mdom_1755, retro_mdom_237, retro_mdom_378, retro_mdom_517, retro_mdom_788, retro_mdom_986,
Oryctolagus cuniculus	ENSOCUG00000028195	5 retrocopies	retro_ocun_110, retro_ocun_136, retro_ocun_175, retro_ocun_22, retro_ocun_46,
Pongo abelii	ENSPPYG00000029777	2 retrocopies	retro_pabe_164, retro_pabe_84,
Pan troglodytes	ENSPTRG00000042199	19 retrocopies	retro_ptro_1004, retro_ptro_1183, retro_ptro_1263, retro_ptro_135, retro_ptro_143, retro_ptro_1775, retro_ptro_2051, retro_ptro_2147, retro_ptro_2212, retro_ptro_2247, retro_ptro_2252, retro_ptro_2400, retro_ptro_2463, retro_ptro_2528, retro_ptro_2605, retro_ptro_2666, retro_ptro_2759, retro_ptro_3260, retro_ptro_65,
Sus scrofa	ENSSSCG00000017212	15 retrocopies	retro_sscr_1112, retro_sscr_1132, retro_sscr_1147, retro_sscr_1148, retro_sscr_123, retro_sscr_249 , retro_sscr_277, retro_sscr_409, retro_sscr_591, retro_sscr_684, retro_sscr_754, retro_sscr_765, retro_sscr_814, retro_sscr_847, retro_sscr_969,
Sus scrofa	ENSSSCG00000024026	2 retrocopies	retro_sscr_1089, retro_sscr_320,