RetrogeneDB ID: retro_sscr_29

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:156760894..156761353(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000011927
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: UBE2A
• Ensembl ID: ENSSSCG00000012621
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2A [Source:HGNC Symbol;Acc:12472]

Sequence

>retro_sscr_29
ATGTCGACCCCGGCCCGGAGGAGACTTATGCGAGATTTCAAGCGATTGCAAGAGGACCCACCTGTGGGTGTCAGTGACGC
ACCATCTGAAAACAACATCATGCAGTGGAATGCAGTTATATTTGGACCAGAAGGGACACCCTTTGAAGATGGTACTTTTA
AACTAGTAATAGAATTTTCTGAAGAATATCCAAATAAACCGCCAACTGTTAGGTTTTTATCCAAAATGTTTCATCCAAAT
GTGTATGCTGATGGTAGCATATGTTTAGATATCCTTCAGAATCGATGGAGTCCAACTTATGATGTATCTTCTATCCTAAC
ATCAATTCAGTCTCTGTTGGATGAACCAAATCCAAACAGTCCAGCCAATAGCCAGGCAGCACAGCTTTATCATGAAAACA
AACGAGAATATGAGAAGAGAGTTTTGGCCATTGTTGAACAAAGCTGGAATGATTCATAA

Alignment

ORF - retro_sscr_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.04 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTPARRRLMRDFKRLQEDPPAGVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTV
          MSTPARRRLMRDFKRLQEDPP.GVS.APSENNIM.WNAVIFGPEGTPFEDGTFKL.IEF.EEYPNKPPTV
Retrocopy MSTPARRRLMRDFKRLQEDPPVGVSDAPSENNIMQWNAVIFGPEGTPFEDGTFKLVIEFSEEYPNKPPTV

Parental  RFVSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKR
          RF.SKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLY.ENKREYEKR
Retrocopy RFLSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYHENKREYEKR

Parental  VSAIVEQSWRD
          V.AIVEQSW.D
Retrocopy VLAIVEQSWND

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	7.17 RPM	15.79 RPM
SRP014902_testis	11.60 RPM	16.97 RPM
SRP018288_heart	32.40 RPM	34.18 RPM
SRP018288_kidney	20.49 RPM	44.23 RPM
SRP018288_liver	15.99 RPM	22.71 RPM
SRP018288_lung	37.27 RPM	32.58 RPM
SRP018856_adipose	33.52 RPM	14.40 RPM
SRP035408_brain	9.05 RPM	62.54 RPM
SRP035408_liver	8.92 RPM	29.47 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_sscr_29 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EW539378	156760985	156761169	100	184	0	184
EW676680	156760980	156761084	100	104	0	104

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_29 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_29 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001079	1 retrocopy	retro_chof_1316,
Callithrix jacchus	ENSCJAG00000005098	2 retrocopies	retro_cjac_1180, retro_cjac_3862,
Cavia porcellus	ENSCPOG00000011908	1 retrocopy	retro_cpor_489,
Dasypus novemcinctus	ENSDNOG00000007060	1 retrocopy	retro_dnov_215,
Macropus eugenii	ENSMEUG00000003026	1 retrocopy	retro_meug_2180,
Monodelphis domestica	ENSMODG00000010209	1 retrocopy	retro_mdom_341,
Oryctolagus cuniculus	ENSOCUG00000016739	1 retrocopy	retro_ocun_183,
Otolemur garnettii	ENSOGAG00000024335	1 retrocopy	retro_ogar_3203,
Procavia capensis	ENSPCAG00000005045	1 retrocopy	retro_pcap_222,
Sus scrofa	ENSSSCG00000012621	1 retrocopy	retro_sscr_29 ,
Tarsius syrichta	ENSTSYG00000000888	1 retrocopy	retro_tsyr_676,