RetrogeneDB ID: retro_cpor_4

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:33437157..33437454(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000001357
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000002336
• Aliases: None
• Description: None

Sequence

>retro_cpor_4
ATGCCTAAGAGGGAGGTCAGCTTAGTCAAAGGGATGGCGAAGGAGGAGTCCAAGAGGAGATCTGCAAGGTTGTCCCCTAA
ACCTGCTCCTGAAAAAGTGGAAATGAAGCCAAGAAAGGCTGAAGGAAAGGATAAATCTTTGGACAAGAAAATGCAAGCAA
AAAGGAAAAGGGGAGAGGAGAAAAAACCATCTGAAGTGCCTAATCTAGAGACCAACCAAGGCTCACCTGCCAAAAATGGA
GAATCGAAAAACAAGGTGAGCTCAGCCTCTGACGAAGCAGAAGAGAAAGATGCCTAG

Alignment

ORF - retro_cpor_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.18 %
• Parental protein coverage: 97.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKRKVSTAAARTAPAPKRRSARLSAKPAPAKVETKPKKAAGKDKSVDKKVQPKGKRGAKGKQAEAAHQE
          MPKR.VS..........KRRSARLS.KPAP.KVE.KP.KA.GKDKS.DKK.Q.K.KRG...K..E....E
Retrocopy MPKREVSLVKGMAKEESKRRSARLSPKPAPEKVEMKPRKAEGKDKSLDKKMQAKRKRGEEKKPSEVPNLE

Parental  AKEDLPAENGEAKNAESAASDEAEEKEA
          .....PA.NGE.KN..S.ASDEAEEK.A
Retrocopy TNQGSPAKNGESKNKVSSASDEAEEKDA

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	31.40 RPM
SRP017611_kidney	0.00 RPM	83.33 RPM
SRP017611_liver	0.00 RPM	23.72 RPM
SRP040447_lung	0.00 RPM	86.23 RPM
SRP040447_skeletal_muscle	0.00 RPM	18.93 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_4 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_4 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 14 parental genes, and 170 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014100	11 retrocopies	retro_amel_1103, retro_amel_1157, retro_amel_1307, retro_amel_1378, retro_amel_1580, retro_amel_1839, retro_amel_349, retro_amel_352, retro_amel_408, retro_amel_439, retro_amel_670,
Bos taurus	ENSBTAG00000018768	12 retrocopies	retro_btau_1178, retro_btau_1475, retro_btau_1560, retro_btau_1746, retro_btau_1801, retro_btau_388, retro_btau_504, retro_btau_572, retro_btau_607, retro_btau_617, retro_btau_897, retro_btau_928,
Canis familiaris	ENSCAFG00000010045	12 retrocopies	retro_cfam_1056, retro_cfam_1233, retro_cfam_1318, retro_cfam_1392, retro_cfam_1522, retro_cfam_1667, retro_cfam_1904, retro_cfam_2202, retro_cfam_292, retro_cfam_404, retro_cfam_634, retro_cfam_649,
Cavia porcellus	ENSCPOG00000002336	7 retrocopies	retro_cpor_1129, retro_cpor_1389, retro_cpor_334, retro_cpor_349, retro_cpor_4 , retro_cpor_884, retro_cpor_949,
Equus caballus	ENSECAG00000019029	5 retrocopies	retro_ecab_1130, retro_ecab_285, retro_ecab_362, retro_ecab_800, retro_ecab_848,
Homo sapiens	ENSG00000205581	7 retrocopies	retro_hsap_1097, retro_hsap_1418, retro_hsap_1581, retro_hsap_1758, retro_hsap_1874, retro_hsap_3370, retro_hsap_762,
Monodelphis domestica	ENSMODG00000020972	5 retrocopies	retro_mdom_1085, retro_mdom_109, retro_mdom_284, retro_mdom_755, retro_mdom_88,
Mustela putorius furo	ENSMPUG00000008550	3 retrocopies	retro_mputfur_252, retro_mputfur_371, retro_mputfur_483,
Mus musculus	ENSMUSG00000040681	13 retrocopies	retro_mmus_1274, retro_mmus_1295, retro_mmus_1445, retro_mmus_1565, retro_mmus_1574, retro_mmus_1636, retro_mmus_2166, retro_mmus_2195, retro_mmus_2895, retro_mmus_3117, retro_mmus_3641, retro_mmus_832, retro_mmus_949,
Otolemur garnettii	ENSOGAG00000010329	35 retrocopies	retro_ogar_1062, retro_ogar_1186, retro_ogar_1245, retro_ogar_1304, retro_ogar_1355, retro_ogar_1437, retro_ogar_1527, retro_ogar_1529, retro_ogar_175, retro_ogar_1812, retro_ogar_1901, retro_ogar_1932, retro_ogar_2057, retro_ogar_2311, retro_ogar_2325, retro_ogar_2522, retro_ogar_2523, retro_ogar_266, retro_ogar_2712, retro_ogar_2729, retro_ogar_278, retro_ogar_2913, retro_ogar_2964, retro_ogar_3095, retro_ogar_3133, retro_ogar_3138, retro_ogar_3155, retro_ogar_333, retro_ogar_3354, retro_ogar_370, retro_ogar_393, retro_ogar_657, retro_ogar_699, retro_ogar_723, retro_ogar_958,
Pongo abelii	ENSPPYG00000011426	25 retrocopies	retro_pabe_1066, retro_pabe_1149, retro_pabe_1172, retro_pabe_1190, retro_pabe_123, retro_pabe_1264, retro_pabe_1302, retro_pabe_1504, retro_pabe_1604, retro_pabe_1842, retro_pabe_2152, retro_pabe_2211, retro_pabe_2284, retro_pabe_2380, retro_pabe_251, retro_pabe_2518, retro_pabe_2771, retro_pabe_3086, retro_pabe_3648, retro_pabe_3825, retro_pabe_504, retro_pabe_698, retro_pabe_699, retro_pabe_702, retro_pabe_760,
Pan troglodytes	ENSPTRG00000031426	22 retrocopies	retro_ptro_1256, retro_ptro_1299, retro_ptro_1301, retro_ptro_1454, retro_ptro_1556, retro_ptro_1740, retro_ptro_1821, retro_ptro_1830, retro_ptro_2058, retro_ptro_2290, retro_ptro_2559, retro_ptro_2716, retro_ptro_3119, retro_ptro_3278, retro_ptro_363, retro_ptro_463, retro_ptro_586, retro_ptro_61, retro_ptro_637, retro_ptro_696, retro_ptro_970, retro_ptro_980,
Rattus norvegicus	ENSRNOG00000048226	8 retrocopies	retro_rnor_1020, retro_rnor_1239, retro_rnor_1290, retro_rnor_2643, retro_rnor_2667, retro_rnor_642, retro_rnor_764, retro_rnor_966,
Rattus norvegicus	ENSRNOG00000050978	5 retrocopies	retro_rnor_1057, retro_rnor_1318, retro_rnor_1389, retro_rnor_2433, retro_rnor_358,