RetrogeneDB ID: retro_sscr_725

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:19258134..19258582(-)
• Located in intron of: ENSSSCG00000022785

Retrocopy information

• Ensembl ID: ENSSSCG00000007813
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL13
• Ensembl ID: ENSSSCG00000024974
• Aliases: None
• Description: ribosomal protein L13 [Source:HGNC Symbol;Acc:10303]

Sequence

>retro_sscr_725
CCGGTGGTGAGATGCCCTATGAAGGTGCGGGCCAACAGAGACCTCAGCCTGGAGGCACTGAGGGTGGCCGGAATCCACAA
GAAAGTGGCCCGGATCTTTGGAATCTCGGTGGATCAGTGGCAGAAGATGCACACGGAGTCCCTGCAGGCCAACGTGCAGC
AGCTCAAGGAGCACTGCTCCAAGCTCATCCTCTTCCCCAGGAAGTCCTCAGCCTCCAAGAAAGGTGACAGCTCTGCTGAA
GAGCTCAAATTGGCCACCCAGCTGACGGGACCAGTCAAGCGCATATGGAACGTGTACCAGAGGGAGAAAGCCAGAGTCAT
TACGGACGAGGAGAAGAGCTTCAAGGCCCTTGACAGTCTCTGCAAGGCCCGTGCCAATGCCTGGCTCTTTGGCATACAGG
CAAAAAAGTGCCAAGGAAGCTGCAGAACAGGATATGGAGAAGAAAAAA

Alignment

ORF - retro_sscr_725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.16 %
• Parental protein coverage: 71.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKCTESLQANVQRLKEYRSKLILFPRKP
          P.VR...KVRA.R..SLE.LRVAGIHKKVAR..GISVD.......TESLQANVQ.LKE..SKLILFPRK.
Retrocopy PVVRCPMKVRANRDLSLEALRVAGIHKKVARIFGISVDQWQKMH-TESLQANVQQLKEHCSKLILFPRKS

Parental  SAPKKGDSSAEELKLATQLTGPVMPIRNVYKREKARVITDEEKNFKAFASLRMARANARLFGIRAKR-AK
          SA.KKGDSSAEELKLATQLTGPV..I.NVY.REKARVITDEEK.FKA..SL..ARANA.LFGI.AK..AK
Retrocopy SASKKGDSSAEELKLATQLTGPVKRIWNVYQREKARVITDEEKSFKALDSLCKARANAWLFGIQAKK>AK

Parental  EAAEQDVEKKK
          EAAEQD.EKKK
Retrocopy EAAEQDMEKKK

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	693.52 RPM
SRP014902_testis	0.00 RPM	1234.40 RPM
SRP018288_heart	0.00 RPM	177.93 RPM
SRP018288_kidney	0.00 RPM	289.41 RPM
SRP018288_liver	0.00 RPM	292.95 RPM
SRP018288_lung	0.00 RPM	247.64 RPM
SRP018856_adipose	0.00 RPM	666.46 RPM
SRP035408_brain	0.03 RPM	289.34 RPM
SRP035408_liver	0.00 RPM	240.66 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_725 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_725 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_725 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017072	1 retrocopy	retro_acar_70,
Ailuropoda melanoleuca	ENSAMEG00000001111	5 retrocopies	retro_amel_1268, retro_amel_1319, retro_amel_188, retro_amel_411, retro_amel_802,
Bos taurus	ENSBTAG00000012044	2 retrocopies	retro_btau_716, retro_btau_817,
Canis familiaris	ENSCAFG00000019840	5 retrocopies	retro_cfam_1135, retro_cfam_1919, retro_cfam_2122, retro_cfam_565, retro_cfam_897,
Callithrix jacchus	ENSCJAG00000009672	5 retrocopies	retro_cjac_2607, retro_cjac_2961, retro_cjac_4054, retro_cjac_663, retro_cjac_747,
Echinops telfairi	ENSETEG00000015057	4 retrocopies	retro_etel_1240, retro_etel_1382, retro_etel_1606, retro_etel_703,
Gorilla gorilla	ENSGGOG00000025427	6 retrocopies	retro_ggor_1548, retro_ggor_1963, retro_ggor_2231, retro_ggor_2732, retro_ggor_562, retro_ggor_767,
Monodelphis domestica	ENSMODG00000003663	4 retrocopies	retro_mdom_1001, retro_mdom_416, retro_mdom_439, retro_mdom_674,
Mus musculus	ENSMUSG00000000740	23 retrocopies	retro_mmus_1091, retro_mmus_1522, retro_mmus_1533, retro_mmus_1854, retro_mmus_2074, retro_mmus_2163, retro_mmus_2186, retro_mmus_2321, retro_mmus_2333, retro_mmus_2351, retro_mmus_25, retro_mmus_2668, retro_mmus_2718, retro_mmus_3097, retro_mmus_3274, retro_mmus_3453, retro_mmus_3489, retro_mmus_3500, retro_mmus_355, retro_mmus_3711, retro_mmus_692, retro_mmus_732, retro_mmus_863,
Ornithorhynchus anatinus	ENSOANG00000006729	1 retrocopy	retro_oana_78,
Rattus norvegicus	ENSRNOG00000015335	14 retrocopies	retro_rnor_1054, retro_rnor_1260, retro_rnor_158, retro_rnor_160, retro_rnor_1719, retro_rnor_1720, retro_rnor_1834, retro_rnor_1848, retro_rnor_2471, retro_rnor_2574, retro_rnor_2608, retro_rnor_2787, retro_rnor_2854, retro_rnor_682,
Sus scrofa	ENSSSCG00000024974	3 retrocopies	retro_sscr_1044, retro_sscr_725 , retro_sscr_884,