RetrogeneDB ID: retro_sscr_742

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:115385159..115385693(-)
• Located in intron of: ENSSSCG00000025901

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPS2
• Ensembl ID: ENSSSCG00000017940
• Aliases: None
• Description: G protein pathway suppressor 2 [Source:HGNC Symbol;Acc:4550]

Sequence

>retro_sscr_742
CAGGAGGAGGAAGAGGTGGACAAGATGATGGGAAAGAAGATGAAGGAAGCACAGGAGAGAAGGGGGAGAAAAAGGAAATA
GCAGAGCAAATGTCACTAGAGGAGACCAAGGAACAAATCCTTAAGTTGCAGGAGGAACTTTCGGCCCTATAGGAAGAGAA
GCAGCAGCTTTTCCTGCAGCTCAAGAAAGTTTTACATGAGGAAGAAAGACAGAGCCAAGGAGCAGGGTGACCTGACCACT
GTGCCATCAGAGGCATACCAGCAAGGCCTGACTGTTCACACAGGAAGTCACCTCCTCATCATGCAGGGGCGCCCTGGAGG
ACCCAAGCGGCCAGGCACCCCACGGCAGCAGACAAAGCCAAAGAGATGTTCGGACTCCAAGTGCTTACGAGCTGGTACTA
GGTGGGCTCAGCAGCTGCTTTCACGGGGACCCCTGAGCAGGGCAATTCCGAGGCAGCCCAGGCAGCGCCTATTGAACTGC
TCAGCCCTCACCTCACTATGGACCCAGCAGCCTCCCTATAGTCCTAGCTCAGAG

Alignment

ORF - retro_sscr_742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.95 %
• Parental protein coverage: 55.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RQEEEEVDKMMEQKMKEEQ-ERRKKKEMEERMSLEETKEQILKLQEKLSALQEEKHQLFLQLKKVLHEEE
          ..EEE....M..........E...KKE..E.MSLEETKEQILKLQE.LSAL.EEK.QLFLQLKKVLHEEE
Retrocopy QEEEEVDKMMGKKMKEAQE<EKGEKKEIAEQMSLEETKEQILKLQEELSAL*EEKQQLFLQLKKVLHEEE

Parental  K-RRRKEQSDLTTLTSAAYQQGLTVHTGTHLLSMQGSPGGHNRPGT-LMAADRAKQMFGPQVLTNRHYVG
          ..R......DLTT..S.AYQQGLTVHTG.HLL.MQG.PGG..RPGT...AAD.AK.MFG.QVLT....VG
Retrocopy R>RAKEQ-GDLTTVPSEAYQQGLTVHTGSHLLIMQGRPGGPKRPGT<PTAADKAKEMFGLQVLTSWY*VG

Parental  SAAAFAGTPEH-GQFQGSPGGAYGTAQPPPHYGPT-QPAYSPSQQ
          SAAAF.GTPE..GQF.GSPG.AY.TAQP.PHYGP..QP.YSPS..
Retrocopy SAAAFTGTPEQ<GQFRGSPGSAY*TAQPSPHYGPS<QPPYSPSSE

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	48.85 RPM
SRP014902_testis	0.00 RPM	41.59 RPM
SRP018288_heart	0.00 RPM	19.62 RPM
SRP018288_kidney	0.00 RPM	34.97 RPM
SRP018288_liver	0.00 RPM	21.91 RPM
SRP018288_lung	0.00 RPM	87.37 RPM
SRP018856_adipose	0.00 RPM	45.63 RPM
SRP035408_brain	0.00 RPM	67.30 RPM
SRP035408_liver	0.00 RPM	33.79 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_742 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_742 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016576	2 retrocopies	retro_amel_1236, retro_amel_362,
Equus caballus	ENSECAG00000010635	2 retrocopies	retro_ecab_124, retro_ecab_480,
Homo sapiens	ENSG00000132522	2 retrocopies	retro_hsap_2738, retro_hsap_4222,
Gorilla gorilla	ENSGGOG00000001672	1 retrocopy	retro_ggor_1907,
Macropus eugenii	ENSMEUG00000010645	2 retrocopies	retro_meug_1327, retro_meug_182,
Myotis lucifugus	ENSMLUG00000026169	1 retrocopy	retro_mluc_1045,
Mus musculus	ENSMUSG00000023170	1 retrocopy	retro_mmus_1476,
Nomascus leucogenys	ENSNLEG00000009364	2 retrocopies	retro_nleu_2477, retro_nleu_600,
Pan troglodytes	ENSPTRG00000023046	1 retrocopy	retro_ptro_1852,
Pteropus vampyrus	ENSPVAG00000005052	1 retrocopy	retro_pvam_35,
Sus scrofa	ENSSSCG00000017940	1 retrocopy	retro_sscr_742 ,