RetrogeneDB ID: retro_cpor_1540

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_95:4109592..4109857(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPC
• Ensembl ID: ENSCPOG00000008563
• Aliases: None
• Description: U1 small nuclear ribonucleoprotein C [Source:UniProtKB/TrEMBL;Acc:H0VCM4]

Sequence

>retro_cpor_1540
AAGACACACTATTACAAATGGATGGAAGAGCAAGGTCAGAGCCTAACTGACAAAACAACAGTTGCATTTCAACAAGAAAA
GATACCTCCTACTCCATTTTGCTCCTCCTCCAGCAGAGGCAATAATCCCATCTCTACCCAGTCTCCTGGGTCTTTCTTAC
CCTGACATAATGCCAGCATCCCATATAGGAGGCCCTCCCATAAAGCCAATGATTGACGCCCCCCCCCCTTCTAAATTGAT
GCCAGTGGGACCTGCTCCCAGAATG

Alignment

ORF - retro_cpor_1540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.11 %
• Parental protein coverage: 54.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPF-SAPPPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMM
          K..Y.KWMEEQ.QSL.DKTT.AFQQ.KIPPTPF...PP.A.A.IP..PSL.G...P..MPA.H.GGPP..
Retrocopy KTHYYKWMEEQGQSLTDKTTVAFQQEKIPPTPF>APPP-AEAIIPSLPSLLGLSYPDIMPASHIGGPPIK

Parental  PMMGPPPPG-MMPVGPAPGM
          PM.........MPVGPAP.M
Retrocopy PMIDXXXXSKLMPVGPAPRM

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	13.86 RPM
SRP017611_kidney	0.00 RPM	25.96 RPM
SRP017611_liver	0.00 RPM	18.11 RPM
SRP040447_lung	0.00 RPM	24.77 RPM
SRP040447_skeletal_muscle	0.00 RPM	29.13 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1540 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1540 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 20 parental genes, and 108 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000963	7 retrocopies	retro_amel_1237, retro_amel_1249, retro_amel_149, retro_amel_1522, retro_amel_1523, retro_amel_592, retro_amel_988,
Canis familiaris	ENSCAFG00000001231	3 retrocopies	retro_cfam_348, retro_cfam_402, retro_cfam_409,
Callithrix jacchus	ENSCJAG00000015321	16 retrocopies	retro_cjac_1009, retro_cjac_1015, retro_cjac_1064, retro_cjac_1750, retro_cjac_1937, retro_cjac_2014, retro_cjac_2395, retro_cjac_2456, retro_cjac_2785, retro_cjac_3056, retro_cjac_3110, retro_cjac_400, retro_cjac_4010, retro_cjac_617, retro_cjac_770, retro_cjac_873,
Cavia porcellus	ENSCPOG00000008563	3 retrocopies	retro_cpor_1529, retro_cpor_1540 , retro_cpor_288,
Felis catus	ENSFCAG00000005876	12 retrocopies	retro_fcat_1008, retro_fcat_1088, retro_fcat_1265, retro_fcat_1545, retro_fcat_1599, retro_fcat_161, retro_fcat_1664, retro_fcat_1814, retro_fcat_446, retro_fcat_578, retro_fcat_627, retro_fcat_922,
Gorilla gorilla	ENSGGOG00000012499	7 retrocopies	retro_ggor_1169, retro_ggor_1333, retro_ggor_1364, retro_ggor_1981, retro_ggor_2577, retro_ggor_2699, retro_ggor_2842,
Myotis lucifugus	ENSMLUG00000002488	8 retrocopies	retro_mluc_1246, retro_mluc_1627, retro_mluc_2020, retro_mluc_2099, retro_mluc_2144, retro_mluc_2332, retro_mluc_735, retro_mluc_962,
Macaca mulatta	ENSMMUG00000000869	9 retrocopies	retro_mmul_1148, retro_mmul_1161, retro_mmul_1343, retro_mmul_1465, retro_mmul_1573, retro_mmul_1626, retro_mmul_2016, retro_mmul_2314, retro_mmul_678,
Monodelphis domestica	ENSMODG00000013904	1 retrocopy	retro_mdom_22,
Mustela putorius furo	ENSMPUG00000003210	7 retrocopies	retro_mputfur_1233, retro_mputfur_1260, retro_mputfur_1396, retro_mputfur_374, retro_mputfur_441, retro_mputfur_519, retro_mputfur_531,
Nomascus leucogenys	ENSNLEG00000008392	2 retrocopies	retro_nleu_2129, retro_nleu_99,
Oryctolagus cuniculus	ENSOCUG00000026668	3 retrocopies	retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii	ENSOGAG00000008755	9 retrocopies	retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Procavia capensis	ENSPCAG00000016885	1 retrocopy	retro_pcap_34,
Pongo abelii	ENSPPYG00000029902	3 retrocopies	retro_pabe_2367, retro_pabe_3397, retro_pabe_3524,
Pan troglodytes	ENSPTRG00000018070	6 retrocopies	retro_ptro_1037, retro_ptro_1283, retro_ptro_1937, retro_ptro_2249, retro_ptro_2606, retro_ptro_2883,
Pteropus vampyrus	ENSPVAG00000015597	1 retrocopy	retro_pvam_1213,
Sarcophilus harrisii	ENSSHAG00000000945	1 retrocopy	retro_shar_112,
Ictidomys tridecemlineatus	ENSSTOG00000013786	3 retrocopies	retro_itri_1278, retro_itri_1374, retro_itri_861,
Tarsius syrichta	ENSTSYG00000011216	6 retrocopies	retro_tsyr_1198, retro_tsyr_1475, retro_tsyr_1746, retro_tsyr_185, retro_tsyr_260, retro_tsyr_690,