RetrogeneDB ID: retro_sscr_1217

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:129002977..129003285(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYCBP
• Ensembl ID: ENSSSCG00000003649
• Aliases: None
• Description: MYC binding protein [Source:HGNC Symbol;Acc:7554]

Sequence

>retro_sscr_1217
ATGACCCATTACAAAGCCACTGACTAAAAGCATGAGCAGTTCCAGAGGTACTTGGAGAAGTCGGGAGTGCTGAACACACT
GACCAAGGTGTCAGTAGCCTTATATGAAGAACCAGAGAAATCTAATAGTGCCTTGAATTTTTTAAGTATCGCTTAGGAGA
TGCTATCCCAGAAAATCCAGAAATAGAGCTGGCTCATCTAGAATTAGCAAAAATGAAAGAGAAATGTGAAGCTATTGTAG
AAGAAAATTAAAAAACTGAAAACAAGTCTTGCTCATATGAACCACTTCAGGAGAAGAAGCATGATGAA

Alignment

ORF - retro_sscr_1217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAHYKAADSKREQFRRYLEKSGVLDTLTKVLVALYEEPEKPNSALDFL-KHHLGAATPENPEIELLRLEL
          M.HYKA.D.K.EQF.RYLEKSGVL.TLTKV.VALYEEPEK.NSAL.FL.K..LG.A.PENPEIEL..LEL
Retrocopy MTHYKATD*KHEQFQRYLEKSGVLNTLTKVSVALYEEPEKSNSALNFL<KYRLGDAIPENPEIELAHLEL

Parental  AEMKEKYEAIVEENKKLKTKLAQYEPPQEEKRAE
          A.MKEK.EAIVEEN.K...K...YEP.QE.K..E
Retrocopy AKMKEKCEAIVEEN*KTENKSCSYEPLQEKKHDE

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	4.51 RPM
SRP014902_testis	0.00 RPM	14.29 RPM
SRP018288_heart	0.00 RPM	8.28 RPM
SRP018288_kidney	0.00 RPM	44.72 RPM
SRP018288_liver	0.00 RPM	28.62 RPM
SRP018288_lung	0.00 RPM	17.11 RPM
SRP018856_adipose	0.00 RPM	8.15 RPM
SRP035408_brain	0.00 RPM	4.26 RPM
SRP035408_liver	0.00 RPM	28.21 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1217 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1217 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030622	1 retrocopy	retro_cfam_1618,
Choloepus hoffmanni	ENSCHOG00000013136	3 retrocopies	retro_chof_1349, retro_chof_151, retro_chof_610,
Callithrix jacchus	ENSCJAG00000036558	1 retrocopy	retro_cjac_5,
Cavia porcellus	ENSCPOG00000020447	1 retrocopy	retro_cpor_1195,
Homo sapiens	ENSG00000214114	2 retrocopies	retro_hsap_1649, retro_hsap_2251,
Gorilla gorilla	ENSGGOG00000005810	2 retrocopies	retro_ggor_1245, retro_ggor_1678,
Loxodonta africana	ENSLAFG00000020514	2 retrocopies	retro_lafr_1071, retro_lafr_903,
Macropus eugenii	ENSMEUG00000000315	1 retrocopy	retro_meug_247,
Mus musculus	ENSMUSG00000028647	1 retrocopy	retro_mmus_1626,
Nomascus leucogenys	ENSNLEG00000011814	2 retrocopies	retro_nleu_1319, retro_nleu_2489,
Oryctolagus cuniculus	ENSOCUG00000022203	2 retrocopies	retro_ocun_907, retro_ocun_979,
Otolemur garnettii	ENSOGAG00000024435	3 retrocopies	retro_ogar_1283, retro_ogar_1553, retro_ogar_1880,
Pongo abelii	ENSPPYG00000001515	1 retrocopy	retro_pabe_1400,
Pan troglodytes	ENSPTRG00000000565	2 retrocopies	retro_ptro_1120, retro_ptro_1594,
Rattus norvegicus	ENSRNOG00000017166	2 retrocopies	retro_rnor_573, retro_rnor_779,
Sus scrofa	ENSSSCG00000003649	2 retrocopies	retro_sscr_1176, retro_sscr_1217 ,
Ictidomys tridecemlineatus	ENSSTOG00000021547	2 retrocopies	retro_itri_1518, retro_itri_252,
Tarsius syrichta	ENSTSYG00000005690	1 retrocopy	retro_tsyr_172,
Tursiops truncatus	ENSTTRG00000009583	1 retrocopy	retro_ttru_1872,