RetrogeneDB ID: retro_sscr_1136

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: JH118875.1:170655..171295(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000026557
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAN
• Ensembl ID: ENSSSCG00000009746
• Aliases: None
• Description: None

Sequence

>retro_sscr_1136
ATGGCTGCCCAAGAACCCCAAGTTCACTTCAACTTGTGTTGGTTGGTAATGGTGGTACTGGGAAAACTGCATTCGTGAAA
CATCATCTGACTGGTGAATTTGAGAAGTATGTAGCTACCTTGGGTGTTGAGGTCCATTCCTTTGTGTTCCATACCAACAG
AGGACCCATTAAGTTGGATGTATGGGACACAGCTGCTCAGGAGAAATTGGGTGGACTGAAAGGTGGCTGTTATATCCAAG
CTCAGTGTGCTGTTATAAAGTTTGATATGACATCAAGAGTTACTTACAAGAACATACCTAACTGGAATAGAGATCTGGTA
CGAGTGTGTGAAAACATCCCCATCGCGTTGTGCGGTAATAAAGTGGATTTTAAGGACAAAGTTTTAAGTCAAAGTTGATT
GTCTTCCACCAAAAGAAGAACCTTCAGTACTATGCTATTTCTGTAGAAAGTAACTACAGTTTTGAAAAGCCCTTCGTCTG
GCTTACTAGAAAACTGATTAGAGATCCTAACGTGGAGTTCATCGCCATGCCTGCTCTTGCCCCACCAGAGGTGGTCATGG
ATCCAGCCTTGGCAGAGCAGTACAAGCAAGATCTAGAGGTTGCTCAGACAACTGCTCTCCTGGACGAAGATGACGACCTG

Alignment

ORF - retro_sscr_1136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAQGEPQVQF-KLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQ
          MAAQ.EPQV.F..LVLVG.GGTGKT.FVK.HLTGEFEK.YVATLGVEVH..VFHTNRGPIK..VWDTA.Q
Retrocopy MAAQ-EPQVHF<QLVLVGNGGTGKTAFVKHHLTGEFEK-YVATLGVEVHSFVFHTNRGPIKLDVWDTAAQ

Parental  EKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDR-KVKAKSIVF
          EK.GGL..G.YIQAQCA.I.FD.TSRVTYKN.PNW.RDLVRVCENIPI.LCGNKVD.KD....K.K.IVF
Retrocopy EKLGGLKGGCYIQAQCAVIKFDMTSRVTYKNIPNWNRDLVRVCENIPIALCGNKVDFKDK<SFKSKLIVF

Parental  HRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTA
          H.KKNLQYY.IS..SNY.FEKPF.WL.RKLI.DPN.EF.AMPALAPPEVVMDPALA.QY..DLEVAQTTA
Retrocopy HQKKNLQYYAISVESNYSFEKPFVWLTRKLIRDPNVEFIAMPALAPPEVVMDPALAEQYKQDLEVAQTTA

Parental  LPDEDDDL
          L.DEDDDL
Retrocopy LLDEDDDL

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	148.53 RPM
SRP014902_testis	0.00 RPM	266.20 RPM
SRP018288_heart	0.00 RPM	124.76 RPM
SRP018288_kidney	0.00 RPM	186.18 RPM
SRP018288_liver	0.00 RPM	172.38 RPM
SRP018288_lung	0.00 RPM	106.82 RPM
SRP018856_adipose	0.00 RPM	195.53 RPM
SRP035408_brain	0.00 RPM	208.51 RPM
SRP035408_liver	0.00 RPM	190.81 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1136 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1136 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 90 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004222	4 retrocopies	retro_amel_1119, retro_amel_1625, retro_amel_1631, retro_amel_700,
Callithrix jacchus	ENSCJAG00000003927	8 retrocopies	retro_cjac_1558, retro_cjac_1844, retro_cjac_2509, retro_cjac_2952, retro_cjac_3071, retro_cjac_3107, retro_cjac_4222, retro_cjac_492,
Echinops telfairi	ENSETEG00000011875	18 retrocopies	retro_etel_1051, retro_etel_1161, retro_etel_1351, retro_etel_1365, retro_etel_1584, retro_etel_1673, retro_etel_1878, retro_etel_1896, retro_etel_1915, retro_etel_2141, retro_etel_2150, retro_etel_2189, retro_etel_294, retro_etel_383, retro_etel_409, retro_etel_412, retro_etel_514, retro_etel_813,
Homo sapiens	ENSG00000132341	3 retrocopies	retro_hsap_3126, retro_hsap_3446, retro_hsap_4908,
Gorilla gorilla	ENSGGOG00000015340	4 retrocopies	retro_ggor_2142, retro_ggor_2328, retro_ggor_2556, retro_ggor_3066,
Loxodonta africana	ENSLAFG00000017673	1 retrocopy	retro_lafr_1253,
Macaca mulatta	ENSMMUG00000020927	2 retrocopies	retro_mmul_1990, retro_mmul_2641,
Monodelphis domestica	ENSMODG00000015601	8 retrocopies	retro_mdom_100, retro_mdom_1718, retro_mdom_1990, retro_mdom_543, retro_mdom_580, retro_mdom_806, retro_mdom_814, retro_mdom_969,
Mus musculus	ENSMUSG00000029430	4 retrocopies	retro_mmus_1653, retro_mmus_182, retro_mmus_2029, retro_mmus_265,
Nomascus leucogenys	ENSNLEG00000008282	4 retrocopies	retro_nleu_1565, retro_nleu_2303, retro_nleu_2353, retro_nleu_775,
Ornithorhynchus anatinus	ENSOANG00000006447	1 retrocopy	retro_oana_62,
Oryctolagus cuniculus	ENSOCUG00000026506	2 retrocopies	retro_ocun_1139, retro_ocun_958,
Otolemur garnettii	ENSOGAG00000025046	8 retrocopies	retro_ogar_1482, retro_ogar_1611, retro_ogar_2058, retro_ogar_2560, retro_ogar_2692, retro_ogar_2810, retro_ogar_377, retro_ogar_497,
Pongo abelii	ENSPPYG00000005124	3 retrocopies	retro_pabe_2582, retro_pabe_2853, retro_pabe_3815,
Pan troglodytes	ENSPTRG00000005636	4 retrocopies	retro_ptro_1762, retro_ptro_2115, retro_ptro_2338, retro_ptro_3273,
Rattus norvegicus	ENSRNOG00000000938	3 retrocopies	retro_rnor_138, retro_rnor_410, retro_rnor_917,
Sarcophilus harrisii	ENSSHAG00000018018	1 retrocopy	retro_shar_538,
Sus scrofa	ENSSSCG00000009746	3 retrocopies	retro_sscr_1136 , retro_sscr_194, retro_sscr_771,
Tursiops truncatus	ENSTTRG00000012732	6 retrocopies	retro_ttru_1481, retro_ttru_204, retro_ttru_387, retro_ttru_439, retro_ttru_792, retro_ttru_892,
Vicugna pacos	ENSVPAG00000008880	3 retrocopies	retro_vpac_436, retro_vpac_589, retro_vpac_85,