RetrogeneDB ID: retro_sscr_335

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:130128680..130129094(+)
• Located in intron of: ENSSSCG00000011772

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM136A
• Ensembl ID: ENSSSCG00000026446
• Aliases: None
• Description: family with sequence similarity 136, member A [Source:HGNC Symbol;Acc:25911]

Sequence

>retro_sscr_335
ATGGCAGAGCTGTAGCAGCTCTAGGTGCAGGAGGCCATGAACTCCATGGTGAAGAATCTGGGGAGAGAGAGCATCCGGAA
GATGCAGGGCCGCATGTTCCGGTGCAGCGCTGGCTGCTGTGAGGACACCCAGGCATCCACTCAGCAGGTGCATCAGTGTA
TTGAGCACTGCCATGCACCTCTGGCTCAAGCCCAGGCCCTGGTCATCAGCGAGTTGGAGAAGGTCCAGGACCACCTGGCC
CAGTGCACTTTGCACTGCAACGACAAGCCAAAGATTTAATAGATGCAGGGAGTAAGGAGATCCAGGTGAAGCGGCAGCTG
GACACTTATGTGACCAAGTGTGTGGATGACCACATGAACCTCATCCCAACCATGACCAAGAAGATGAAGGAGTCGGCTCC
CGTCCATGGGGAAA

Alignment

ORF - retro_sscr_335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAELQQLRVQEAVDSMVKNLERENIRKMQGLMFRCSAGCCEDSQASMQQVHQCIERCHAPLAQAQALVTS
          MAEL.QL.VQEA..SMVKNL.RE.IRKMQG.MFRCSAGCCED.QAS.QQVHQCIE.CHAPLAQAQALV.S
Retrocopy MAEL*QL*VQEAMNSMVKNLGRESIRKMQGRMFRCSAGCCEDTQASTQQVHQCIEHCHAPLAQAQALVIS

Parental  ELEKFQDRLARCTLHCNDK-AKDSIDAGSKELQVKRQLECCVTKCVDDHMNLIPTMTKKMKES-LSSMGK
          ELEK.QD.LA.CTLHCNDK.AKD.IDAGSKE.QVKRQL...VTKCVDDHMNLIPTMTKKMKES.L.SMGK
Retrocopy ELEKVQDHLAQCTLHCNDK<AKDLIDAGSKEIQVKRQLDTYVTKCVDDHMNLIPTMTKKMKES>LPSMGK

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	11.55 RPM
SRP014902_testis	0.28 RPM	45.97 RPM
SRP018288_heart	0.00 RPM	25.17 RPM
SRP018288_kidney	0.10 RPM	43.15 RPM
SRP018288_liver	0.00 RPM	37.90 RPM
SRP018288_lung	0.00 RPM	21.69 RPM
SRP018856_adipose	0.02 RPM	24.17 RPM
SRP035408_brain	0.06 RPM	31.82 RPM
SRP035408_liver	0.06 RPM	58.65 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_335 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_335 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015992	1 retrocopy	retro_amel_1454,
Bos taurus	ENSBTAG00000008674	2 retrocopies	retro_btau_37, retro_btau_88,
Canis familiaris	ENSCAFG00000003353	2 retrocopies	retro_cfam_1042, retro_cfam_148,
Cavia porcellus	ENSCPOG00000009117	1 retrocopy	retro_cpor_221,
Dasypus novemcinctus	ENSDNOG00000019447	7 retrocopies	retro_dnov_2036, retro_dnov_2465, retro_dnov_2612, retro_dnov_324, retro_dnov_620, retro_dnov_873, retro_dnov_901,
Dipodomys ordii	ENSDORG00000006529	4 retrocopies	retro_dord_365, retro_dord_391, retro_dord_733, retro_dord_778,
Felis catus	ENSFCAG00000008119	1 retrocopy	retro_fcat_1459,
Homo sapiens	ENSG00000035141	5 retrocopies	retro_hsap_1855, retro_hsap_2599, retro_hsap_2683, retro_hsap_3136, retro_hsap_3413,
Gorilla gorilla	ENSGGOG00000023247	6 retrocopies	retro_ggor_1361, retro_ggor_1625, retro_ggor_2155, retro_ggor_2356, retro_ggor_53, retro_ggor_8,
Macropus eugenii	ENSMEUG00000015791	8 retrocopies	retro_meug_1126, retro_meug_1351, retro_meug_1545, retro_meug_167, retro_meug_2131, retro_meug_219, retro_meug_457, retro_meug_719,
Macaca mulatta	ENSMMUG00000007962	5 retrocopies	retro_mmul_1421, retro_mmul_1772, retro_mmul_220, retro_mmul_327, retro_mmul_656,
Monodelphis domestica	ENSMODG00000011533	1 retrocopy	retro_mdom_65,
Mus musculus	ENSMUSG00000057497	2 retrocopies	retro_mmus_240, retro_mmus_3101,
Otolemur garnettii	ENSOGAG00000028265	4 retrocopies	retro_ogar_1788, retro_ogar_2273, retro_ogar_379, retro_ogar_684,
Pongo abelii	ENSPPYG00000012323	6 retrocopies	retro_pabe_1512, retro_pabe_1917, retro_pabe_2297, retro_pabe_2618, retro_pabe_2828, retro_pabe_3032,
Pan troglodytes	ENSPTRG00000012030	6 retrocopies	retro_ptro_1237, retro_ptro_1523, retro_ptro_1809, retro_ptro_2120, retro_ptro_2318, retro_ptro_3063,
Rattus norvegicus	ENSRNOG00000016273	1 retrocopy	retro_rnor_1679,
Sus scrofa	ENSSSCG00000026446	6 retrocopies	retro_sscr_1075, retro_sscr_229, retro_sscr_230, retro_sscr_309, retro_sscr_335 , retro_sscr_914,
Ictidomys tridecemlineatus	ENSSTOG00000008343	1 retrocopy	retro_itri_1026,
Tupaia belangeri	ENSTBEG00000017418	8 retrocopies	retro_tbel_1377, retro_tbel_1875, retro_tbel_2479, retro_tbel_2516, retro_tbel_3373, retro_tbel_3703, retro_tbel_401, retro_tbel_999,
Tursiops truncatus	ENSTTRG00000001198	5 retrocopies	retro_ttru_1110, retro_ttru_1771, retro_ttru_1903, retro_ttru_396, retro_ttru_550,