RetrogeneDB ID: retro_cpor_825

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:16649284..16649603(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL22
• Ensembl ID: ENSCPOG00000020139
• Aliases: None
• Description: None

Sequence

>retro_cpor_825
TTCACCCCTGACTGCGCACATCCTGGAGAAGACAGAATCATGGATACTGCCAATTTTGAGCAGTTTCTCCAGGAGAGAAT
CCACATGAGCAGCAAAGCTGGGAATCTCAGTAGCAGGGGCATTCACCATCAAAAGGAGATAGAGCAAAATCATCATGACT
TCCAAAGCGCTTCTCTCCAAAAGGTATTTGAAATATCTCAACAAAAAATATTTGAAGAAGAATAATCCACATGATTAGTT
GTGCATAGTCACTAGCAGCAAAGAGAGATGAATTATATTACTTCCAGATTAACAGGAGGAAGAAGAGGAGGAAGATGAG

Alignment

ORF - retro_cpor_825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.94 %
• Parental protein coverage: 82.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGG-GVVTIERSKSKITVTSEVPFSKRYLKYLTKK
          FT.DC.HP.ED.IMD.ANFEQFLQERI....KAGNL...G..TI.R..SKI..TS....SKRYLKYL.KK
Retrocopy FTPDCAHPGEDRIMDTANFEQFLQERIHMSSKAGNLSS>GAFTIKRR*SKIIMTSKALLSKRYLKYLNKK

Parental  YLKKNNLRDWLRVVANSKESYELRYFQINQDEEEEED
          YLKKNN..D.L..V..SKE............EEEE..
Retrocopy YLKKNNPHD*LCIVTSSKER*IILLPD*QEEEEEEDE

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
SRP017611_brain	0.00 RPM	34.80 RPM
SRP017611_kidney	0.00 RPM	57.68 RPM
SRP017611_liver	0.00 RPM	48.31 RPM
SRP040447_lung	0.00 RPM	65.52 RPM
SRP040447_skeletal_muscle	0.00 RPM	49.24 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_825 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_825 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 93 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009864	7 retrocopies	retro_amel_1219, retro_amel_1247, retro_amel_1775, retro_amel_1793, retro_amel_369, retro_amel_830, retro_amel_870,
Bos taurus	ENSBTAG00000014423	4 retrocopies	retro_btau_1491, retro_btau_566, retro_btau_694, retro_btau_892,
Cavia porcellus	ENSCPOG00000009215	1 retrocopy	retro_cpor_1544,
Cavia porcellus	ENSCPOG00000020139	2 retrocopies	retro_cpor_825 , retro_cpor_837,
Gorilla gorilla	ENSGGOG00000027739	10 retrocopies	retro_ggor_1111, retro_ggor_1652, retro_ggor_1655, retro_ggor_1708, retro_ggor_1757, retro_ggor_2268, retro_ggor_2567, retro_ggor_37, retro_ggor_531, retro_ggor_613,
Macaca mulatta	ENSMMUG00000018347	12 retrocopies	retro_mmul_1004, retro_mmul_1044, retro_mmul_1047, retro_mmul_1512, retro_mmul_2209, retro_mmul_2264, retro_mmul_2467, retro_mmul_2601, retro_mmul_271, retro_mmul_445, retro_mmul_469, retro_mmul_80,
Mustela putorius furo	ENSMPUG00000007087	6 retrocopies	retro_mputfur_1074, retro_mputfur_1277, retro_mputfur_134, retro_mputfur_1433, retro_mputfur_578, retro_mputfur_873,
Pongo abelii	ENSPPYG00000001951	11 retrocopies	retro_pabe_1196, retro_pabe_1213, retro_pabe_1435, retro_pabe_166, retro_pabe_248, retro_pabe_3114, retro_pabe_349, retro_pabe_3782, retro_pabe_3817, retro_pabe_590, retro_pabe_966,
Sus scrofa	ENSSSCG00000003367	4 retrocopies	retro_sscr_257, retro_sscr_276, retro_sscr_497, retro_sscr_509,
Ictidomys tridecemlineatus	ENSSTOG00000002832	4 retrocopies	retro_itri_1250, retro_itri_1326, retro_itri_1543, retro_itri_407,
Tarsius syrichta	ENSTSYG00000003649	32 retrocopies	retro_tsyr_1043, retro_tsyr_1086, retro_tsyr_1140, retro_tsyr_1163, retro_tsyr_1197, retro_tsyr_1259, retro_tsyr_1304, retro_tsyr_1338, retro_tsyr_1350, retro_tsyr_1524, retro_tsyr_1587, retro_tsyr_1788, retro_tsyr_1966, retro_tsyr_1978, retro_tsyr_200, retro_tsyr_2075, retro_tsyr_2101, retro_tsyr_2114, retro_tsyr_219, retro_tsyr_242, retro_tsyr_337, retro_tsyr_377, retro_tsyr_392, retro_tsyr_504, retro_tsyr_688, retro_tsyr_788, retro_tsyr_828, retro_tsyr_881, retro_tsyr_969, retro_tsyr_972, retro_tsyr_973, retro_tsyr_983,