RetrogeneDB ID: retro_cpor_1366

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_72:4010035..4010573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL7
• Ensembl ID: ENSCPOG00000004140
• Aliases: None
• Description: None

Sequence

>retro_cpor_1366
AAGGCAAGGAGGAAGCTCATCTATGCAAAAGCCAGGCACTGTCATAAAGGGTAGAGACAGATGTACAGACCCAAGATTCA
AATCACTAGGGTGGCAACAGAAGCCGGCAACTTCTATGTACCTGCAGAACCCAAATTGGCATCTGTCATCCGGATCAGGG
ATATCGATGGTGTGAGCCCCAAAGTCCACAAGGTTCGGCAGCTTTTTCTTTGTCTTTGCCAAATGCCCAATGGTACCTTT
GTTAAGCTCCACAAGGCTTCATTTAACACGCTGAGGATTGTGGGATCATATATGGCATGCGGATGCCCAAAGGTGAAGTC
AGTAAATGAACTCACATACAAGCCGGCTATAACAAAATCAACCAGAAGTGAACTGCCTTGACGATAATTCACTGACTGCT
CGAGCTCTTGGTAAATATGGCATCATCTGCACGGAGGATCTGATTCGTAAGATCTATGCTGTTGGAAAATGCTTCAGAGA
GGCAAATAACTTCCTGTGGCCCTTCGAATTATCATCTCCCGGAGGTGGAATGAATAAG

Alignment

ORF - retro_cpor_1366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.98 %
• Parental protein coverage: 86.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KARRKLIYEKARHYHKEYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQL-L
          KARRKLIY.KARH.HK..RQMYR..I...R.A..AGNFYVPAEPKLA.VIRIR.I.GVSPKV.KV.QL.L
Retrocopy KARRKLIYAKARHCHKG*RQMYRPKIQITRVATEAGNFYVPAEPKLASVIRIRDIDGVSPKVHKVRQLFL

Parental  RLRQIFNGTFVKLNKASVNMLRIVEPYIAWGYPNLKSVNELIYK-RGYGKINKKRIALT-DNSLIARSLG
          .L.Q..NGTFVKL.KAS.N.LRIV..Y.A.G.P..KSVNEL.YK..GY.KIN.K..ALT.DNSL.AR.LG
Retrocopy CLCQMPNGTFVKLHKASFNTLRIVGSYMACGCPKVKSVNELTYK<AGYNKINQK*TALT<DNSLTARALG

Parental  KYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKK
          KYGIIC.EDLI..IY.VGK.F.EANNFLWPF.LSSP.GGM.K
Retrocopy KYGIICTEDLIRKIYAVGKCFREANNFLWPFELSSPGGGMNK

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	185.03 RPM
SRP017611_kidney	0.21 RPM	270.09 RPM
SRP017611_liver	0.09 RPM	197.22 RPM
SRP040447_lung	0.05 RPM	309.49 RPM
SRP040447_skeletal_muscle	0.00 RPM	315.34 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1366 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1366 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 10 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004140	18 retrocopies	retro_cpor_1056, retro_cpor_1190, retro_cpor_1342, retro_cpor_1347, retro_cpor_1348, retro_cpor_1366 , retro_cpor_1418, retro_cpor_1449, retro_cpor_1452, retro_cpor_1453, retro_cpor_187, retro_cpor_209, retro_cpor_245, retro_cpor_266, retro_cpor_397, retro_cpor_458, retro_cpor_506, retro_cpor_640,
Cavia porcellus	ENSCPOG00000021189	2 retrocopies	retro_cpor_1134, retro_cpor_653,
Erinaceus europaeus	ENSEEUG00000010307	3 retrocopies	retro_eeur_354, retro_eeur_420, retro_eeur_55,
Echinops telfairi	ENSETEG00000005656	33 retrocopies	retro_etel_1099, retro_etel_1120, retro_etel_1154, retro_etel_1158, retro_etel_1333, retro_etel_1370, retro_etel_1553, retro_etel_1642, retro_etel_1708, retro_etel_1720, retro_etel_175, retro_etel_185, retro_etel_1891, retro_etel_2042, retro_etel_2044, retro_etel_2118, retro_etel_2149, retro_etel_265, retro_etel_316, retro_etel_375, retro_etel_402, retro_etel_519, retro_etel_532, retro_etel_554, retro_etel_610, retro_etel_793, retro_etel_865, retro_etel_869, retro_etel_877, retro_etel_887, retro_etel_889, retro_etel_992, retro_etel_993,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Mustela putorius furo	ENSMPUG00000010240	15 retrocopies	retro_mputfur_1004, retro_mputfur_1031, retro_mputfur_1034, retro_mputfur_1035, retro_mputfur_1156, retro_mputfur_1168, retro_mputfur_1384, retro_mputfur_1454, retro_mputfur_1481, retro_mputfur_390, retro_mputfur_410, retro_mputfur_545, retro_mputfur_839, retro_mputfur_929, retro_mputfur_982,
Nomascus leucogenys	ENSNLEG00000026615	8 retrocopies	retro_nleu_1012, retro_nleu_1459, retro_nleu_1696, retro_nleu_1853, retro_nleu_2479, retro_nleu_2603, retro_nleu_3, retro_nleu_901,
Sorex araneus	ENSSARG00000001088	3 retrocopies	retro_sara_268, retro_sara_310, retro_sara_623,