RetrogeneDB ID: retro_cpor_1216

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_58:1374514..1374913(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFN1
• Ensembl ID: ENSCPOG00000013136
• Aliases: None
• Description: Profilin [Source:UniProtKB/TrEMBL;Acc:H0VN18]

Sequence

>retro_cpor_1216
GCGGGGCTGAGGGAGTGCCAGCACGGCCTCCTGGTGGGTGGAACCTGTCAGGACCCGGCCATTGTGGGCCACAAGCACTA
GCCCTCTGTTTGGACCTTGGAACCCGGTAAAGTCTTCGTCAGTGTCACACCAGCTAAAGGCGCTGTCCTGGTTGGCAAAG
ACTGGTCGTTTTTTGTGTGAATGGGTTGGCACTTGGAGACCAGAAGTGCCGTGTGATCCAGAACTCACTGCTGCAGAATT
TACCGCGGGATCTTCACACCAAGAGCGCGGGTGGGCCTCCACGTTCAGCATCACTGTCGCCACGACCGCCATGACGCTCG
TCCTGCTGATGGGCAAAGAAGGCGTCCGAGGTGTACAGTCAACAAGAAATGCTATGAAGTGGACTCCCACCTGCGGCGC

Alignment

ORF - retro_cpor_1216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.15 %
• Parental protein coverage: 97.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKIFVNITPAEVAVLVGKDRASFF-VNGLTLGGQK
          AG.......L...GTCQD.AIVG.K..PSVW...PGK.FV..TPA..AVLVGKD...F..VNGL.LG.QK
Retrocopy AGLRECQHGLLVGGTCQDPAIVGHKH*PSVWTLEPGKVFVSVTPAKGAVLVGKDWSFFV<VNGLALGDQK

Parental  CSVIRDSLLQDGEFTMDLRTKSTGGAP-TFNVTVTMTAKTLVLLMGKEGVHGGM-INKKCYEMASHLRR
          C.VI..SLLQ......DL.TKS.GG.P.TF..TV..TA.TLVLLMGKEGV.G....NKKCYE..SHLRR
Retrocopy CRVIQNSLLQN--LPRDLHTKSAGGPP<TFSITVATTAMTLVLLMGKEGVRGVQ<VNKKCYEVDSHLRR

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	49.87 RPM
SRP017611_kidney	0.00 RPM	144.15 RPM
SRP017611_liver	0.00 RPM	144.47 RPM
SRP040447_lung	0.05 RPM	441.64 RPM
SRP040447_skeletal_muscle	0.03 RPM	101.52 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1216 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1216 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 19 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006193	2 retrocopies	retro_amel_1712, retro_amel_1781,
Bos taurus	ENSBTAG00000004915	1 retrocopy	retro_btau_141,
Callithrix jacchus	ENSCJAG00000011719	2 retrocopies	retro_cjac_1023, retro_cjac_1641,
Cavia porcellus	ENSCPOG00000013136	1 retrocopy	retro_cpor_1216 ,
Equus caballus	ENSECAG00000021116	3 retrocopies	retro_ecab_171, retro_ecab_28, retro_ecab_559,
Homo sapiens	ENSG00000108518	10 retrocopies	retro_hsap_214, retro_hsap_215, retro_hsap_221, retro_hsap_223, retro_hsap_224, retro_hsap_352, retro_hsap_446, retro_hsap_447, retro_hsap_450, retro_hsap_451,
Gorilla gorilla	ENSGGOG00000022394	3 retrocopies	retro_ggor_285, retro_ggor_289, retro_ggor_366,
Macaca mulatta	ENSMMUG00000002772	5 retrocopies	retro_mmul_407, retro_mmul_527, retro_mmul_528, retro_mmul_574, retro_mmul_732,
Mus musculus	ENSMUSG00000018293	1 retrocopy	retro_mmus_1326,
Nomascus leucogenys	ENSNLEG00000017446	6 retrocopies	retro_nleu_16, retro_nleu_1870, retro_nleu_2425, retro_nleu_2429, retro_nleu_848, retro_nleu_886,
Otolemur garnettii	ENSOGAG00000031395	3 retrocopies	retro_ogar_1680, retro_ogar_2143, retro_ogar_3351,
Procavia capensis	ENSPCAG00000000291	1 retrocopy	retro_pcap_27,
Pelodiscus sinensis	ENSPSIG00000004124	1 retrocopy	retro_psin_8,
Pan troglodytes	ENSPTRG00000008616	5 retrocopies	retro_ptro_185, retro_ptro_196, retro_ptro_276, retro_ptro_332, retro_ptro_333,
Rattus norvegicus	ENSRNOG00000003975	1 retrocopy	retro_rnor_1623,
Sus scrofa	ENSSSCG00000017905	1 retrocopy	retro_sscr_275,
Ictidomys tridecemlineatus	ENSSTOG00000028950	1 retrocopy	retro_itri_129,
Tursiops truncatus	ENSTTRG00000001299	1 retrocopy	retro_ttru_14,
Vicugna pacos	ENSVPAG00000005327	3 retrocopies	retro_vpac_389, retro_vpac_395, retro_vpac_457,