RetrogeneDB ID: retro_sscr_894

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:11818881..11819258(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000001060
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HINT1
• Ensembl ID: ENSSSCG00000014264
• Aliases: None
• Description: histidine triad nucleotide binding protein 1 [Source:HGNC Symbol;Acc:4912]

Sequence

>retro_sscr_894
ATGGCAGATGGGATTGCCAAGGCTCAGGCCGCCGGGCCTGGTGGCGATACGATCTTCGGGAAGGTCATTGGCAAGGAAAT
GCCGGCCAAAATCGCTTCTGAGGATGCTCAGTGTCTTGCTTTCCATGACATCTCCCCTCGAGCGCCAACACATTTTCTGG
CGATAGCCAAGAAATGCACATCTCAGATTCTGCCGCAGAGGACGACGGTGAAAGCCTCCTTGGACATTGAATGATGGTCG
GCAAGAAATGTGCCGCTGACCTGGGCCTGAAAGAAGGGTTATCGGATGGAGTGATGGAAGGTTCAGATGGGGGACAGTCT
GTCTATCATGTTCATCGCCATGTTCTTGGAGGCGGGCAGATGGACTGGCCTCCTGGG

Alignment

ORF - retro_sscr_894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADEIAKAQAARPGGDTIFGKIIRKEIPAKIIYEDDQCLAFHDISPQAPTHFLVIPKKHISQI-SAAEDD
          MAD.IAKAQAA.PGGDTIFGK.I.KE.PAKI..ED.QCLAFHDISP.APTHFL.I.KK..SQI.SAAEDD
Retrocopy MADGIAKAQAAGPGGDTIFGKVIGKEMPAKIASEDAQCLAFHDISPRAPTHFLAIAKKCTSQI<SAAEDD

Parental  DESLLGHLMIVGKKCAADLGLKKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMNWPPG
          .ESLLGH.M.VGKKCAADLGLK.G....V.EGSDGGQSVYHVH.HVLGG.QM.WPPG
Retrocopy GESLLGH*MMVGKKCAADLGLKEGLSDGVMEGSDGGQSVYHVHRHVLGGGQMDWPPG

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	80.20 RPM
SRP018288_heart	0.00 RPM	100.69 RPM
SRP018288_kidney	0.00 RPM	254.74 RPM
SRP018288_liver	0.00 RPM	238.43 RPM
SRP018288_lung	0.00 RPM	65.98 RPM
SRP018856_adipose	0.00 RPM	126.44 RPM
SRP035408_brain	0.00 RPM	283.78 RPM
SRP035408_liver	0.00 RPM	92.32 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_894 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_894 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017774	4 retrocopies	retro_amel_1426, retro_amel_1657, retro_amel_460, retro_amel_511,
Bos taurus	ENSBTAG00000010959	5 retrocopies	retro_btau_1036, retro_btau_1149, retro_btau_1782, retro_btau_926, retro_btau_978,
Canis familiaris	ENSCAFG00000032152	1 retrocopy	retro_cfam_473,
Callithrix jacchus	ENSCJAG00000014398	3 retrocopies	retro_cjac_134, retro_cjac_142, retro_cjac_87,
Echinops telfairi	ENSETEG00000010127	1 retrocopy	retro_etel_1,
Gorilla gorilla	ENSGGOG00000011967	1 retrocopy	retro_ggor_89,
Macropus eugenii	ENSMEUG00000005368	2 retrocopies	retro_meug_1001, retro_meug_848,
Myotis lucifugus	ENSMLUG00000001091	2 retrocopies	retro_mluc_1388, retro_mluc_2100,
Monodelphis domestica	ENSMODG00000028727	3 retrocopies	retro_mdom_102, retro_mdom_1741, retro_mdom_286,
Mustela putorius furo	ENSMPUG00000011639	4 retrocopies	retro_mputfur_1337, retro_mputfur_1376, retro_mputfur_45, retro_mputfur_93,
Oryctolagus cuniculus	ENSOCUG00000006607	5 retrocopies	retro_ocun_1374, retro_ocun_214, retro_ocun_643, retro_ocun_821, retro_ocun_968,
Rattus norvegicus	ENSRNOG00000000622	1 retrocopy	retro_rnor_98,
Sarcophilus harrisii	ENSSHAG00000005834	2 retrocopies	retro_shar_113, retro_shar_301,
Sus scrofa	ENSSSCG00000014264	2 retrocopies	retro_sscr_371, retro_sscr_894 ,
Ictidomys tridecemlineatus	ENSSTOG00000027920	4 retrocopies	retro_itri_1129, retro_itri_114, retro_itri_177, retro_itri_260,
Tursiops truncatus	ENSTTRG00000008653	4 retrocopies	retro_ttru_1364, retro_ttru_1660, retro_ttru_217, retro_ttru_349,