RetrogeneDB ID: retro_sscr_1026

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:69313347..69313622(+)
• Located in intron of: ENSSSCG00000024613

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIGD1A
• Ensembl ID: ENSSSCG00000011290
• Aliases: None
• Description: HIG1 hypoxia inducible domain family, member 1A [Source:HGNC Symbol;Acc:29527]

Sequence

>retro_sscr_1026
ATGTCAACCAACATAGATATTTCCCTTTCTTCATATGATGAAGATCATGGATCTAAATTTATCTGAAAAGCTAGAGGGGC
ACAATTTGTCCCTGTTGGAATGGCAGGTTTTGCAGCAATCACTGCATATTGATTAGATAAGCTGAAGATCAGGGGGGATA
CTAAAATTTCTGTTCAACTGTTTCACATGTGCATGGCAGCCCAAAGCTTTGTTGTGAAAGCATGATTCTTGATATGGACT
ACTCCATATATGAGGAATTCCAGGCAAAACCTAAA

Alignment

ORF - retro_sscr_1026 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.82 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTDTDVSLSSYDEDQGSKLIRKAKEAPFVPIGMAGFAAIVAYGLYKLKSRGNTKMSVHLIHMRVAAQGF
          MST..D.SLSSYDED.GSK.I.KA..A.FVP.GMAGFAAI.AY.L.KLK.RG.TK.SV.L.HM..AAQ.F
Retrocopy MSTNIDISLSSYDEDHGSKFI*KARGAQFVPVGMAGFAAITAY*LDKLKIRGDTKISVQLFHMCMAAQSF

Parental  VVGA-MTLGMGYSMYREFWAKPK
          VV.A.M.L.M.YS.Y.EF.AKPK
Retrocopy VVKA<MILDMDYSIYEEFQAKPK

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	14.20 RPM
SRP014902_testis	0.00 RPM	12.73 RPM
SRP018288_heart	0.00 RPM	168.32 RPM
SRP018288_kidney	0.00 RPM	114.46 RPM
SRP018288_liver	0.00 RPM	129.21 RPM
SRP018288_lung	0.00 RPM	14.36 RPM
SRP018856_adipose	0.00 RPM	14.90 RPM
SRP035408_brain	0.00 RPM	76.51 RPM
SRP035408_liver	0.00 RPM	40.10 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1026 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1026 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1026 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 114 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012431	1 retrocopy	retro_amel_679,
Choloepus hoffmanni	ENSCHOG00000009079	10 retrocopies	retro_chof_1067, retro_chof_1609, retro_chof_171, retro_chof_180, retro_chof_1978, retro_chof_2028, retro_chof_2253, retro_chof_495, retro_chof_546, retro_chof_81,
Callithrix jacchus	ENSCJAG00000032668	9 retrocopies	retro_cjac_1056, retro_cjac_1703, retro_cjac_3001, retro_cjac_3044, retro_cjac_3211, retro_cjac_4111, retro_cjac_514, retro_cjac_79, retro_cjac_920,
Cavia porcellus	ENSCPOG00000000703	11 retrocopies	retro_cpor_1263, retro_cpor_1517, retro_cpor_314, retro_cpor_347, retro_cpor_420, retro_cpor_800, retro_cpor_973, retro_cpor_974, retro_cpor_975, retro_cpor_976, retro_cpor_977,
Equus caballus	ENSECAG00000010978	1 retrocopy	retro_ecab_755,
Echinops telfairi	ENSETEG00000007493	4 retrocopies	retro_etel_1278, retro_etel_1741, retro_etel_1957, retro_etel_767,
Felis catus	ENSFCAG00000000537	2 retrocopies	retro_fcat_1479, retro_fcat_414,
Homo sapiens	ENSG00000181061	13 retrocopies	retro_hsap_1003, retro_hsap_1221, retro_hsap_1313, retro_hsap_205, retro_hsap_2391, retro_hsap_2411, retro_hsap_2969, retro_hsap_3269, retro_hsap_391, retro_hsap_3975, retro_hsap_4079, retro_hsap_884, retro_hsap_996,
Gorilla gorilla	ENSGGOG00000016759	3 retrocopies	retro_ggor_1025, retro_ggor_148, retro_ggor_951,
Macaca mulatta	ENSMMUG00000018783	11 retrocopies	retro_mmul_1093, retro_mmul_1296, retro_mmul_2057, retro_mmul_2164, retro_mmul_2298, retro_mmul_495, retro_mmul_568, retro_mmul_603, retro_mmul_792, retro_mmul_804, retro_mmul_966,
Monodelphis domestica	ENSMODG00000013605	6 retrocopies	retro_mdom_1618, retro_mdom_176, retro_mdom_1937, retro_mdom_1988, retro_mdom_948, retro_mdom_970,
Mustela putorius furo	ENSMPUG00000011870	3 retrocopies	retro_mputfur_1112, retro_mputfur_1287, retro_mputfur_892,
Mus musculus	ENSMUSG00000038412	1 retrocopy	retro_mmus_249,
Otolemur garnettii	ENSOGAG00000011358	3 retrocopies	retro_ogar_1546, retro_ogar_2641, retro_ogar_2844,
Ochotona princeps	ENSOPRG00000016072	1 retrocopy	retro_opri_564,
Pongo abelii	ENSPPYG00000013974	16 retrocopies	retro_pabe_1014, retro_pabe_1096, retro_pabe_1776, retro_pabe_2159, retro_pabe_2196, retro_pabe_2462, retro_pabe_2707, retro_pabe_3136, retro_pabe_3199, retro_pabe_322, retro_pabe_3269, retro_pabe_3348, retro_pabe_398, retro_pabe_434, retro_pabe_672, retro_pabe_841,
Pan troglodytes	ENSPTRG00000014802	1 retrocopy	retro_ptro_89,
Rattus norvegicus	ENSRNOG00000019428	1 retrocopy	retro_rnor_36,
Sus scrofa	ENSSSCG00000011290	1 retrocopy	retro_sscr_1026 ,
Ictidomys tridecemlineatus	ENSSTOG00000009681	3 retrocopies	retro_itri_1636, retro_itri_775, retro_itri_879,
Tupaia belangeri	ENSTBEG00000002324	5 retrocopies	retro_tbel_1136, retro_tbel_1451, retro_tbel_1608, retro_tbel_1991, retro_tbel_4525,
Tursiops truncatus	ENSTTRG00000009760	8 retrocopies	retro_ttru_1001, retro_ttru_1090, retro_ttru_120, retro_ttru_1292, retro_ttru_330, retro_ttru_362, retro_ttru_632, retro_ttru_79,