RetrogeneDB ID: retro_cpor_1261

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_60:3118285..3118758(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF4
• Ensembl ID: ENSCPOG00000010334
• Aliases: None
• Description: None

Sequence

>retro_cpor_1261
ATGGGCCTCACCATCTCCTGGCTCTTCTCCTGCCTCTTCGGCCAGAAGCAAATATGTATTTGGATGGTTGGACTGGATGC
TGTTGGCAAGACAACCATTCTATATCAACTCAAGTTAGGGAAGCTAGTCACCACCATTCCTACCCTTGATTTTAATGTGG
GAACAGCAGAATATAGGAACATTTGTTTCACAGTCTGGGACGTTGGTGGTCAAGATAAAATTAGGCCTCTCTGGAAGCAT
TACTTTGAGAATACACAGGGTCTTATTTTTGTGGTAGATACCAATGCTCCTGAAAGAATTCAGGAAGGAGAAACATCCTG
CAGAATCTGCTTCAGAAAGATGAGCTGCACGATGCAGTGCTGTTGCTTTTTGTGAACAAATGGGGTTTGCCAAAAGCTAT
GGCCGTCAGTGAAATGACACCGAGTCTTCAGTCTCTTCCTAACAGAACATGGTATGTTCAAGCTGCTTGTGCT

Alignment

ORF - retro_cpor_1261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.4 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGLTISSLFSRLFGKKQMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNICFTVWDVGG
          MGLTIS.LFS.LFG.KQ..I.MVGLDA.GKTTILY.LKLG..VTTIPT..FNV.T.EY.NICFTVWDVGG
Retrocopy MGLTISWLFSCLFGQKQICIWMVGLDAVGKTTILYQLKLGKLVTTIPTLDFNVGTAEYRNICFTVWDVGG

Parental  QDKIRPLWRHYFQNTQGLIFVVDSNDRERIQEG-ANVLQSMLQEDELQDAVLLLFANKQDLPNAMAISEM
          QDKIRPLW.HYF.NTQGLIFVVD.N..ERIQEG..N.LQ..LQ.DEL.DAVLLLF.NK..LP.AMA.SEM
Retrocopy QDKIRPLWKHYFENTQGLIFVVDTNAPERIQEG<RNILQNLLQKDELHDAVLLLFVNKWGLPKAMAVSEM

Parental  TDKLGLQSLRNRTWYVQATCA
          T....LQSL.NRTWYVQA.CA
Retrocopy TP--SLQSLPNRTWYVQAACA

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	0.06 RPM	38.08 RPM
SRP017611_kidney	0.00 RPM	74.43 RPM
SRP017611_liver	0.00 RPM	46.05 RPM
SRP040447_lung	0.00 RPM	73.54 RPM
SRP040447_skeletal_muscle	0.00 RPM	19.71 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1261 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1261 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 26 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016069	1 retrocopy	retro_btau_542,
Choloepus hoffmanni	ENSCHOG00000006427	4 retrocopies	retro_chof_1024, retro_chof_1807, retro_chof_2368, retro_chof_36,
Ciona intestinalis	ENSCING00000021790	1 retrocopy	retro_cint_10,
Callithrix jacchus	ENSCJAG00000019922	1 retrocopy	retro_cjac_507,
Cavia porcellus	ENSCPOG00000010334	1 retrocopy	retro_cpor_1261 ,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Cavia porcellus	ENSCPOG00000025074	1 retrocopy	retro_cpor_92,
Dipodomys ordii	ENSDORG00000004312	1 retrocopy	retro_dord_731,
Homo sapiens	ENSG00000168374	2 retrocopies	retro_hsap_1296, retro_hsap_4221,
Gorilla gorilla	ENSGGOG00000000294	1 retrocopy	retro_ggor_1552,
Microcebus murinus	ENSMICG00000002015	3 retrocopies	retro_mmur_1528, retro_mmur_1558, retro_mmur_360,
Myotis lucifugus	ENSMLUG00000007990	1 retrocopy	retro_mluc_2272,
Macaca mulatta	ENSMMUG00000018617	1 retrocopy	retro_mmul_50,
Monodelphis domestica	ENSMODG00000000185	1 retrocopy	retro_mdom_1538,
Nomascus leucogenys	ENSNLEG00000007270	3 retrocopies	retro_nleu_2106, retro_nleu_2703, retro_nleu_2704,
Oryctolagus cuniculus	ENSOCUG00000000824	4 retrocopies	retro_ocun_1007, retro_ocun_1502, retro_ocun_1868, retro_ocun_987,
Otolemur garnettii	ENSOGAG00000012034	4 retrocopies	retro_ogar_1407, retro_ogar_1501, retro_ogar_2963, retro_ogar_764,
Pongo abelii	ENSPPYG00000013768	3 retrocopies	retro_pabe_1013, retro_pabe_1075, retro_pabe_3451,
Pan troglodytes	ENSPTRG00000015051	2 retrocopies	retro_ptro_2866, retro_ptro_888,
Rattus norvegicus	ENSRNOG00000012623	2 retrocopies	retro_rnor_1036, retro_rnor_1884,
Sorex araneus	ENSSARG00000009272	1 retrocopy	retro_sara_681,
Ictidomys tridecemlineatus	ENSSTOG00000019470	2 retrocopies	retro_itri_1439, retro_itri_1614,
Tupaia belangeri	ENSTBEG00000007415	1 retrocopy	retro_tbel_2075,
Tarsius syrichta	ENSTSYG00000009748	1 retrocopy	retro_tsyr_2059,
Tursiops truncatus	ENSTTRG00000015381	1 retrocopy	retro_ttru_284,
Vicugna pacos	ENSVPAG00000003891	1 retrocopy	retro_vpac_459,