RetrogeneDB ID: retro_cpor_406

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_143:1110396..1110742(+)
• Located in intron of: ENSCPOG00000015419

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBIZ
• Ensembl ID: ENSCPOG00000005819
• Aliases: None
• Description: Ubiquitin-40S ribosomal protein S27a Ubiquitin 40S ribosomal protein S27a [Source:UniProtKB/Swiss-Prot;Acc:P62978]

Sequence

>retro_cpor_406
GTTGAACCCTCATATACTATAGAAAATATAAAGGCTGAGATTCAGGATAAGGAAGGAATTCCTCCTAATCATCAAAGGCT
GATCTTTGCTGTTATGCAAGTGGAAGATGGATGTACTTTGTCTGATTACAAAGAGTCAGCCCTTCATCTTACATGGAGAC
TCTGTAATGGTGCTGAGAAAAGAAAGAAATCTTATATTCCCTCCAAGAAAAATAAGCATAAGAGAAGTTTAAGCTGGTTC
TGAAATAGTACAAGGTAGATAAAAATGACCAGGTTAGTCACCTTCATTAAGATTACCCTTCAGATGAATGTGGGGCTGGA
GTTTCATGGCCACTGGCATGACCAGG

Alignment

ORF - retro_cpor_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.9 %
• Parental protein coverage: 78.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGAKKRKKKSYT
          VEPS.TIEN.KA.IQDKEGIPP..QRLIFA..Q.EDG.TLSDY...KES.LHL..RL..GA.KRKK.SY.
Retrocopy VEPSYTIENIKAEIQDKEGIPPNHQRLIFAVMQVEDGCTLSDY---KESALHLTWRLCNGAEKRKK-SYI

Parental  TPKKNKHKRK-KVKLAVLKYYKVDENGKISRLRRECPSDECGAGV-FMASHFDR
          .P.K.......K.KL.VLK.YKVD.N...S.L....PSDECGAGV.FMA....R
Retrocopy -PSKKNKHKR<KFKL-VLK*YKVDKNDQVSHLH*DYPSDECGAGV<FMATGMTR

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	0.40 RPM	139.13 RPM
SRP017611_kidney	0.42 RPM	181.95 RPM
SRP017611_liver	0.52 RPM	119.39 RPM
SRP040447_lung	0.50 RPM	178.79 RPM
SRP040447_skeletal_muscle	0.01 RPM	156.32 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_406 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_406 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 17 parental genes, and 193 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004017	5 retrocopies	retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Canis familiaris	ENSCAFG00000023471	3 retrocopies	retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus	ENSCJAG00000010052	5 retrocopies	retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Cavia porcellus	ENSCPOG00000005819	7 retrocopies	retro_cpor_1040, retro_cpor_1433, retro_cpor_406 , retro_cpor_409, retro_cpor_502, retro_cpor_591, retro_cpor_990,
Dasypus novemcinctus	ENSDNOG00000004813	12 retrocopies	retro_dnov_131, retro_dnov_1340, retro_dnov_1432, retro_dnov_1558, retro_dnov_1664, retro_dnov_2022, retro_dnov_2183, retro_dnov_2576, retro_dnov_2635, retro_dnov_491, retro_dnov_538, retro_dnov_771,
Dipodomys ordii	ENSDORG00000006291	11 retrocopies	retro_dord_114, retro_dord_13, retro_dord_372, retro_dord_396, retro_dord_430, retro_dord_472, retro_dord_478, retro_dord_549, retro_dord_584, retro_dord_662, retro_dord_737,
Erinaceus europaeus	ENSEEUG00000002329	9 retrocopies	retro_eeur_127, retro_eeur_143, retro_eeur_193, retro_eeur_283, retro_eeur_289, retro_eeur_308, retro_eeur_58, retro_eeur_629, retro_eeur_72,
Gorilla gorilla	ENSGGOG00000007678	9 retrocopies	retro_ggor_1290, retro_ggor_1291, retro_ggor_1502, retro_ggor_1749, retro_ggor_179, retro_ggor_203, retro_ggor_2373, retro_ggor_2858, retro_ggor_2885,
Loxodonta africana	ENSLAFG00000023133	2 retrocopies	retro_lafr_1122, retro_lafr_185,
Myotis lucifugus	ENSMLUG00000017064	10 retrocopies	retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus	ENSMLUG00000029449	1 retrocopy	retro_mluc_1585,
Macaca mulatta	ENSMMUG00000015563	8 retrocopies	retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica	ENSMODG00000001819	3 retrocopies	retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Oryctolagus cuniculus	ENSOCUG00000003613	10 retrocopies	retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Pongo abelii	ENSPPYG00000025871	1 retrocopy	retro_pabe_117,
Rattus norvegicus	ENSRNOG00000004426	2 retrocopies	retro_rnor_117, retro_rnor_161,
Tupaia belangeri	ENSTBEG00000004626	95 retrocopies	retro_tbel_1019, retro_tbel_1022, retro_tbel_1057, retro_tbel_1058, retro_tbel_106, retro_tbel_1081, retro_tbel_1086, retro_tbel_1090, retro_tbel_1134, retro_tbel_1255, retro_tbel_1385, retro_tbel_1403, retro_tbel_1459, retro_tbel_1493, retro_tbel_1565, retro_tbel_1566, retro_tbel_157, retro_tbel_1584, retro_tbel_1606, retro_tbel_1623, retro_tbel_1673, retro_tbel_1678, retro_tbel_1760, retro_tbel_1825, retro_tbel_1863, retro_tbel_1902, retro_tbel_1946, retro_tbel_1952, retro_tbel_2067, retro_tbel_2119, retro_tbel_2122, retro_tbel_2123, retro_tbel_2238, retro_tbel_2354, retro_tbel_2408, retro_tbel_2605, retro_tbel_2671, retro_tbel_2739, retro_tbel_283, retro_tbel_2913, retro_tbel_2939, retro_tbel_2952, retro_tbel_3056, retro_tbel_3119, retro_tbel_3120, retro_tbel_3125, retro_tbel_3180, retro_tbel_3183, retro_tbel_3213, retro_tbel_3258, retro_tbel_3260, retro_tbel_3283, retro_tbel_3389, retro_tbel_3446, retro_tbel_3480, retro_tbel_3481, retro_tbel_3505, retro_tbel_3576, retro_tbel_3595, retro_tbel_3621, retro_tbel_3649, retro_tbel_3665, retro_tbel_3831, retro_tbel_3839, retro_tbel_3840, retro_tbel_3874, retro_tbel_3920, retro_tbel_396, retro_tbel_3977, retro_tbel_4021, retro_tbel_4053, retro_tbel_4133, retro_tbel_4149, retro_tbel_4224, retro_tbel_426, retro_tbel_4284, retro_tbel_4305, retro_tbel_4313, retro_tbel_4474, retro_tbel_4484, retro_tbel_4498, retro_tbel_4499, retro_tbel_4502, retro_tbel_4504, retro_tbel_4547, retro_tbel_4554, retro_tbel_4565, retro_tbel_4628, retro_tbel_703, retro_tbel_709, retro_tbel_763, retro_tbel_843, retro_tbel_866, retro_tbel_871, retro_tbel_874,