RetrogeneDB ID: retro_sscr_941

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:67953701..67954322(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA2
• Ensembl ID: ENSSSCG00000002876
• Aliases: None
• Description: ubiquitin-like modifier activating enzyme 2 [Source:HGNC Symbol;Acc:30661]

Sequence

>retro_sscr_941
GCACTGTGTCAGGGGCTGTGCCTGGAACTGGCCAGGGCTGTGGCCAGTGGCTGGGTCCTGGTGGTGGGCACGGATAGCAT
GGCTGCAAGCTCCTAAAAAACCCCTTGTGCTCAGCGGTTTCTCACACATCGACTCGATTGATCTGGATACTATTGATGTC
AGCAACCTCAACAGACAGTTTTGTTTCAAAAGAAACATGTTGGAAGATCAAAGGCCCAGGTTGCCAAAGAAAGCGTCCTG
CAGTTTTACCCAAAAGCTAATATCATAGTCTACCTTGACAGCATCATGAACCCTGACTATACTGTGGAATTTTTTCGACA
ATTTATATTGGTTATGAATGCTTTAGATAACAGAGCTGCCTGCAACCATGTTAACAGAATGTGTCTAGCAGCAGACGTCC
CTCTTACTGAGAGTGGAACTGCTAGTCATCTTGGGCAAGTAACCACTATCAAAAAGGATGTGACTGAGTGTTATGAATGT
CATCCCAAACCAACCCAGAGAACTTTTCCCAGCTGTACAATTTGTAATACACCTTCAGAACCTATTCATTGCATCATTTG
AGCAAAACATTCATTCAACCAGTTGTTTGGGGAAGAAGATGCTGATCAAGAAGTATCTCCT

Alignment

ORF - retro_sscr_941 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.25 %
• Parental protein coverage: 89.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALSRGLPRELAEAVAGGRVLVVGAGGIGCELLKN-LVLTGFSHIDLIDLDTIDVSNLNRQF-LFQKKHVG
          AL..GL..ELA.AVA.G.VLVVG.........K..LVL.GFSHID.IDLDTIDVSNLNRQF.LFQKKHVG
Retrocopy ALCQGLCLELARAVASGWVLVVGTDSMAASS*KT>LVLSGFSHIDSIDLDTIDVSNLNRQF<LFQKKHVG

Parental  RSKAQVAKESVLQFYPKANIIAYHDSIMNPDYNVEFFRQFILVMNALDNRAARNHVNRMCLAADVPLIES
          RSKAQVAKESVLQFYPKANII.Y.DSIMNPDY.VEFFRQFILVMNALDNRAA.NHVNRMCLAADVPL.ES
Retrocopy RSKAQVAKESVLQFYPKANIIVYLDSIMNPDYTVEFFRQFILVMNALDNRAACNHVNRMCLAADVPLTES

Parental  GTAGYLGQVTTIKKGVTECYECHPKPTQRTFPGCTIRNTPSEPIHCIVWAKYLFNQLFGEEDADQEVSP
          GTA..LGQVTTIKK.VTECYECHPKPTQRTFP.CTI.NTPSEPIHCI..AK..FNQLFGEEDADQEVSP
Retrocopy GTASHLGQVTTIKKDVTECYECHPKPTQRTFPSCTICNTPSEPIHCII*AKHSFNQLFGEEDADQEVSP

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	5.84 RPM
SRP014902_testis	0.14 RPM	27.02 RPM
SRP018288_heart	0.00 RPM	12.89 RPM
SRP018288_kidney	0.00 RPM	12.61 RPM
SRP018288_liver	0.00 RPM	8.64 RPM
SRP018288_lung	0.00 RPM	13.44 RPM
SRP018856_adipose	0.02 RPM	10.21 RPM
SRP035408_brain	0.00 RPM	7.59 RPM
SRP035408_liver	0.00 RPM	6.69 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_941 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_941 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_941 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011975	3 retrocopies	retro_chof_1034, retro_chof_548, retro_chof_848,
Myotis lucifugus	ENSMLUG00000003047	1 retrocopy	retro_mluc_286,
Monodelphis domestica	ENSMODG00000011934	1 retrocopy	retro_mdom_1509,
Pongo abelii	ENSPPYG00000009837	1 retrocopy	retro_pabe_304,
Rattus norvegicus	ENSRNOG00000021113	1 retrocopy	retro_rnor_939,
Sus scrofa	ENSSSCG00000002876	1 retrocopy	retro_sscr_941 ,