RetrogeneDB ID: retro_sscr_188

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:209761490..209761720(-)
• Located in intron of: ENSSSCG00000025013

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP1LC3B
• Ensembl ID: ENSSSCG00000002655
• Aliases: None
• Description: Sus scrofa microtubule-associated protein 1 light chain 3 beta (MAP1LC3B), mRNA. [Source:RefSeq mRNA;Acc:NM_001190290]

Sequence

>retro_sscr_188
ATGCCACCAGAAAAAACCTTCAAACAACGTCCAGCCTTTGAACAAAGAGTAGAAGATGTCCTCCTTATCCAAGAGCAGCA
TCCTACCAAAATCCTAGTAATAGTAGAACTATACAAAGGTGAGAAGCTGCTTCTAGTCCTGGATAAAACAGAGTTCCTGG
TGCCTGATCATGTCAACATGAGTGAGATCATCAGGATAATTAGAAGGCCTTATAGCTCAACACTAATCAG

Alignment

ORF - retro_sscr_188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.21 %
• Parental protein coverage: 61.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRR-
          MP.EKTFKQR..FEQRVEDV.LI.EQHPTKI.VI.E.YKGEK.L.VLDKT.FLVPDHVNMSE.I.IIRR.
Retrocopy MPPEKTFKQRPAFEQRVEDVLLIQEQHPTKILVIVELYKGEKLLLVLDKTEFLVPDHVNMSEIIRIIRR<

Parental  RLQLNANQ
          .L.LN.NQ
Retrocopy AL*LNTNQ

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	62.78 RPM
SRP014902_testis	0.00 RPM	44.98 RPM
SRP018288_heart	0.00 RPM	76.17 RPM
SRP018288_kidney	0.00 RPM	107.27 RPM
SRP018288_liver	0.00 RPM	99.46 RPM
SRP018288_lung	0.00 RPM	48.88 RPM
SRP018856_adipose	0.00 RPM	96.21 RPM
SRP035408_brain	0.00 RPM	81.15 RPM
SRP035408_liver	0.00 RPM	58.07 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_188 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_188 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_188 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 31 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018254	2 retrocopies	retro_amel_1660, retro_amel_873,
Bos taurus	ENSBTAG00000011632	1 retrocopy	retro_btau_977,
Canis familiaris	ENSCAFG00000019909	1 retrocopy	retro_cfam_1578,
Choloepus hoffmanni	ENSCHOG00000012090	7 retrocopies	retro_chof_146, retro_chof_2230, retro_chof_2274, retro_chof_2432, retro_chof_510, retro_chof_558, retro_chof_960,
Callithrix jacchus	ENSCJAG00000004473	3 retrocopies	retro_cjac_1114, retro_cjac_1519, retro_cjac_779,
Cavia porcellus	ENSCPOG00000023922	1 retrocopy	retro_cpor_394,
Dasypus novemcinctus	ENSDNOG00000010228	7 retrocopies	retro_dnov_1008, retro_dnov_1024, retro_dnov_1335, retro_dnov_165, retro_dnov_2435, retro_dnov_2604, retro_dnov_913,
Dipodomys ordii	ENSDORG00000013862	1 retrocopy	retro_dord_376,
Echinops telfairi	ENSETEG00000015189	2 retrocopies	retro_etel_1050, retro_etel_3,
Felis catus	ENSFCAG00000001938	4 retrocopies	retro_fcat_1727, retro_fcat_1874, retro_fcat_340, retro_fcat_884,
Homo sapiens	ENSG00000140941	3 retrocopies	retro_hsap_3695, retro_hsap_487, retro_hsap_62,
Loxodonta africana	ENSLAFG00000023364	3 retrocopies	retro_lafr_1077, retro_lafr_915, retro_lafr_974,
Microcebus murinus	ENSMICG00000007356	2 retrocopies	retro_mmur_117, retro_mmur_507,
Myotis lucifugus	ENSMLUG00000015596	1 retrocopy	retro_mluc_1586,
Macaca mulatta	ENSMMUG00000017613	1 retrocopy	retro_mmul_15,
Mus musculus	ENSMUSG00000031812	4 retrocopies	retro_mmus_1271, retro_mmus_2384, retro_mmus_2619, retro_mmus_846,
Nomascus leucogenys	ENSNLEG00000011511	4 retrocopies	retro_nleu_1032, retro_nleu_1467, retro_nleu_2392, retro_nleu_931,
Oryctolagus cuniculus	ENSOCUG00000022970	4 retrocopies	retro_ocun_1155, retro_ocun_572, retro_ocun_731, retro_ocun_784,
Otolemur garnettii	ENSOGAG00000004256	3 retrocopies	retro_ogar_1468, retro_ogar_2885, retro_ogar_2892,
Ochotona princeps	ENSOPRG00000015461	4 retrocopies	retro_opri_1136, retro_opri_369, retro_opri_85, retro_opri_977,
Pongo abelii	ENSPPYG00000007628	7 retrocopies	retro_pabe_1280, retro_pabe_1566, retro_pabe_245, retro_pabe_3157, retro_pabe_3158, retro_pabe_940, retro_pabe_978,
Pan troglodytes	ENSPTRG00000008445	3 retrocopies	retro_ptro_2505, retro_ptro_367, retro_ptro_63,
Pteropus vampyrus	ENSPVAG00000016858	1 retrocopy	retro_pvam_728,
Rattus norvegicus	ENSRNOG00000017905	5 retrocopies	retro_rnor_1240, retro_rnor_1739, retro_rnor_1865, retro_rnor_1868, retro_rnor_2033,
Sarcophilus harrisii	ENSSHAG00000017074	1 retrocopy	retro_shar_168,
Sus scrofa	ENSSSCG00000002655	2 retrocopies	retro_sscr_188 , retro_sscr_737,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Ictidomys tridecemlineatus	ENSSTOG00000014826	2 retrocopies	retro_itri_1505, retro_itri_662,
Tupaia belangeri	ENSTBEG00000001165	11 retrocopies	retro_tbel_1008, retro_tbel_1644, retro_tbel_2020, retro_tbel_2484, retro_tbel_2561, retro_tbel_3181, retro_tbel_3301, retro_tbel_636, retro_tbel_706, retro_tbel_733, retro_tbel_990,
Tursiops truncatus	ENSTTRG00000008821	2 retrocopies	retro_ttru_1336, retro_ttru_1454,
Vicugna pacos	ENSVPAG00000010065	2 retrocopies	retro_vpac_169, retro_vpac_186,