RetrogeneDB ID: retro_cpor_1310

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_69:1471985..1472517(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSCPOG00000021174
• Aliases: None
• Description: None

Sequence

>retro_cpor_1310
AATAGCTTAGCTAATCTCTTCAAGAGACCTTTTGGAACAAAAGGAGTATGCATTCTCATGGTAGGCCTGGATGCTGCCAT
GAAGACAACCATTCTATACAAACTGAAGCTTGGTGAAATTATGAGCACCATTCCTACCATAGGTTTCAATGTAGAGACGG
TTGAATACAAGAACATCAAGTTCTCCGTGTGAAACGTGGGTGGCCATGACAAGATCCAGTGACTATGGTGCCACTACATC
CAGAACTTCCAAGCTTGATCTTTATGATAGGTAGCAATGACAGAGAGCATATAAACGATGCCTGTGAGAAGCTCATGAAG
ATGCTGGCCAAAGACAACTTCTGAGATGCTGTCCTCCTCACATTTGTCAATAAGCAGGACCTCCCCAGTATGATATATGT
AGCAGAAATCAGACACAGCTGGGGCTGCACTCTCTACACCACAGGAACTGGTACATTCAGCCTATTTGTCCCACCAAAGG
GATTCGGATCTATGAAGAACTGGACTGACTGTTCAACTAGCTAAGCAACAGA

Alignment

ORF - retro_cpor_1310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.11 %
• Parental protein coverage: 98.34 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQD
          N..ANLFK..FG.K...ILMVGLDAA.KTTILYKLKLGEI..TIPTIGFNVETVEYKNI.F.V..VGG.D
Retrocopy NSLANLFKRPFGTKGVCILMVGLDAAMKTTILYKLKLGEIMSTIPTIGFNVETVEYKNIKFSV*NVGGHD

Parental  KIRPLWRHYFQNTQ-GLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEI-T
          KI..LW.HY.QN.Q..LIF...SNDRE..N.A.E.LM.MLA.D...DAVLL.F.NKQDLP.....AEI..
Retrocopy KIQ*LWCHYIQNFQ<SLIFMIGSNDREHINDACEKLMKMLAKDNF*DAVLLTFVNKQDLPSMIYVAEI<Q

Parental  DKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQ
          ..LGLHSL.HRNWYIQ..C.T.G...YE.LD.L.N.L.N.
Retrocopy TQLGLHSLHHRNWYIQPICPTKGIRIYEELD*LFN*LSNR

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	104.68 RPM
SRP017611_kidney	0.00 RPM	142.48 RPM
SRP017611_liver	0.00 RPM	84.92 RPM
SRP040447_lung	0.00 RPM	172.89 RPM
SRP040447_skeletal_muscle	0.00 RPM	102.50 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1310 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1310 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 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus	ENSCPOG00000010334	1 retrocopy	retro_cpor_1261,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310 ,
Cavia porcellus	ENSCPOG00000025074	1 retrocopy	retro_cpor_92,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000029374	1 retrocopy	retro_fcat_1829,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gorilla gorilla	ENSGGOG00000011263	5 retrocopies	retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Tupaia belangeri	ENSTBEG00000009218	9 retrocopies	retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000014186	2 retrocopies	retro_ttru_1679, retro_ttru_347,