RetrogeneDB ID: retro_sscr_1004

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:89395626..89395880(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL37
• Ensembl ID: ENSSSCG00000025883
• Aliases: None
• Description: ribosomal protein L37 [Source:HGNC Symbol;Acc:10347]

Sequence

>retro_sscr_1004
AAGCTTCAGAATAAGATGCACACGTTGAGCTGCTCTAAGCCCTGCCATCTTCAGAAGTCAACCTGTGGCACATGCGGCTA
CCCCGCCAGGCGAAAGAGAAAATATCACCAGAGTGCTGAAGCTAAAAGATGAAATACCGCTGGACTGGTTGAATGCGGCA
CCTAAAAATTGTGTGTGGCAGATTCAGGCATGGATTTCGTGAAGGAACAACACCTAAACCCAAGAGGGCAGCAGCTGTGG
CATCCAGTTCATCT

Alignment

ORF - retro_sscr_1004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.28 %
• Parental protein coverage: 90.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTG-TGRMRHLKIVYRRFRHGF
          K..NK.HTL...C.SK..HLQKSTCG.CGYPA.RKRKY..SA.AKR.NT.G.TG.MRHLKIV..RFRHGF
Retrocopy KLQNKMHTLS--C-SKPCHLQKSTCGTCGYPARRKRKYHQSAEAKR*NTAG<TG*MRHLKIVCGRFRHGF

Parental  REGTTPKPKRAAVAASSSS
          REGTTPKPKRAA..ASSSS
Retrocopy REGTTPKPKRAAAVASSSS

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	569.55 RPM
SRP014902_testis	0.00 RPM	2139.24 RPM
SRP018288_heart	0.00 RPM	318.38 RPM
SRP018288_kidney	0.00 RPM	345.66 RPM
SRP018288_liver	0.00 RPM	317.26 RPM
SRP018288_lung	0.00 RPM	690.48 RPM
SRP018856_adipose	0.00 RPM	1378.84 RPM
SRP035408_brain	0.00 RPM	723.95 RPM
SRP035408_liver	0.00 RPM	476.97 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1004 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1004 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005142	6 retrocopies	retro_btau_1430, retro_btau_1502, retro_btau_1575, retro_btau_1670, retro_btau_181, retro_btau_243,
Callithrix jacchus	ENSCJAG00000007388	10 retrocopies	retro_cjac_107, retro_cjac_1443, retro_cjac_169, retro_cjac_2091, retro_cjac_2443, retro_cjac_247, retro_cjac_2495, retro_cjac_2654, retro_cjac_2956, retro_cjac_332,
Latimeria chalumnae	ENSLACG00000002787	1 retrocopy	retro_lcha_6,
Loxodonta africana	ENSLAFG00000030052	13 retrocopies	retro_lafr_1101, retro_lafr_1123, retro_lafr_1125, retro_lafr_1136, retro_lafr_215, retro_lafr_374, retro_lafr_448, retro_lafr_507, retro_lafr_532, retro_lafr_619, retro_lafr_775, retro_lafr_985, retro_lafr_986,
Macaca mulatta	ENSMMUG00000023807	6 retrocopies	retro_mmul_1602, retro_mmul_1672, retro_mmul_206, retro_mmul_329, retro_mmul_976, retro_mmul_997,
Monodelphis domestica	ENSMODG00000020301	3 retrocopies	retro_mdom_130, retro_mdom_1843, retro_mdom_942,
Mus musculus	ENSMUSG00000041841	28 retrocopies	retro_mmus_1333, retro_mmus_1360, retro_mmus_1425, retro_mmus_1560, retro_mmus_1717, retro_mmus_1732, retro_mmus_1804, retro_mmus_1813, retro_mmus_2067, retro_mmus_2379, retro_mmus_2385, retro_mmus_2513, retro_mmus_2559, retro_mmus_2575, retro_mmus_2691, retro_mmus_2811, retro_mmus_2838, retro_mmus_3090, retro_mmus_3222, retro_mmus_3343, retro_mmus_3345, retro_mmus_3364, retro_mmus_3455, retro_mmus_3493, retro_mmus_3503, retro_mmus_3504, retro_mmus_3674, retro_mmus_438,
Oryctolagus cuniculus	ENSOCUG00000029674	11 retrocopies	retro_ocun_1063, retro_ocun_1269, retro_ocun_1476, retro_ocun_1491, retro_ocun_1514, retro_ocun_1870, retro_ocun_295, retro_ocun_683, retro_ocun_771, retro_ocun_879, retro_ocun_956,
Otolemur garnettii	ENSOGAG00000034300	7 retrocopies	retro_ogar_127, retro_ogar_1308, retro_ogar_1662, retro_ogar_1667, retro_ogar_2670, retro_ogar_662, retro_ogar_76,
Rattus norvegicus	ENSRNOG00000012538	6 retrocopies	retro_rnor_171, retro_rnor_181, retro_rnor_220, retro_rnor_246, retro_rnor_321, retro_rnor_325,
Sus scrofa	ENSSSCG00000025883	5 retrocopies	retro_sscr_1004 , retro_sscr_1220, retro_sscr_1221, retro_sscr_767, retro_sscr_872,