RetrogeneDB ID: retro_cpor_525

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_18:13978312..13978640(-)
• Located in intron of: ENSCPOG00000013371

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2A2
• Ensembl ID: ENSCPOG00000000816
• Aliases: None
• Description: Transcription initiation factor IIA subunit 2 [Source:UniProtKB/TrEMBL;Acc:H0UUS7]

Sequence

>retro_cpor_525
GTGGCCCATCAGTTACACAGGAATACTACCTTGGGAAATAGTCTTGAGGAGAGCCTAGATGAGCTCACATAAGTTTCAAC
ATATGACCCTTCAACTTGCCCTGCAAGTTCTACTTCAATTTGATAAGCCTACAAATTCAGGATTGGCGCAGAGGGTATGG
AACAGAGTCAGATTCTGGAGCTTTCTAAATATGTACAGATTCTGTGATGATGTGTGGACTTTTGTAATGAATGATGTTGA
ATTCAGAGAGGTGACAGAACTTATTAATGTGGATAAAGTGAAATCTGTAGTGTGCAATGGTAAAAATACTGGCTCTAATA
CTACAGAA

Alignment

ORF - retro_cpor_525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.36 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAYQLYRNTTLGNSLQESLDELI-QSQQITPQLALQVLLQFDKAINSALAQRVRNRVNFRGSLNTYRFCD
          .A.QL.RNTTLGNSL.ESLDEL....Q..T.QLALQVLLQFDK..NS.LAQRV.NRV.F...LN.YRFCD
Retrocopy VAHQLHRNTTLGNSLEESLDELT>KFQHMTLQLALQVLLQFDKPTNSGLAQRVWNRVRFWSFLNMYRFCD

Parental  NVWTFVLNDVEFREVTELIKVDKVKIVACDGKNTGSNTTE
          .VWTFV.NDVEFREVTELI.VDKVK.V.C.GKNTGSNTTE
Retrocopy DVWTFVMNDVEFREVTELINVDKVKSVVCNGKNTGSNTTE

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	14.67 RPM
SRP017611_kidney	0.00 RPM	30.05 RPM
SRP017611_liver	0.00 RPM	11.71 RPM
SRP040447_lung	0.00 RPM	16.22 RPM
SRP040447_skeletal_muscle	0.00 RPM	14.78 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_525 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_525 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 16 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010298	1 retrocopy	retro_btau_1649,
Canis familiaris	ENSCAFG00000016665	2 retrocopies	retro_cfam_786, retro_cfam_912,
Cavia porcellus	ENSCPOG00000000816	1 retrocopy	retro_cpor_525 ,
Dipodomys ordii	ENSDORG00000007867	3 retrocopies	retro_dord_377, retro_dord_385, retro_dord_695,
Homo sapiens	ENSG00000140307	1 retrocopy	retro_hsap_4034,
Macaca mulatta	ENSMMUG00000018428	1 retrocopy	retro_mmul_2303,
Monodelphis domestica	ENSMODG00000011636	1 retrocopy	retro_mdom_1563,
Otolemur garnettii	ENSOGAG00000007061	1 retrocopy	retro_ogar_1752,
Ochotona princeps	ENSOPRG00000012841	1 retrocopy	retro_opri_908,
Pan troglodytes	ENSPTRG00000007129	1 retrocopy	retro_ptro_2734,
Rattus norvegicus	ENSRNOG00000011062	2 retrocopies	retro_rnor_1021, retro_rnor_1141,
Sorex araneus	ENSSARG00000012228	2 retrocopies	retro_sara_607, retro_sara_734,
Sus scrofa	ENSSSCG00000004583	3 retrocopies	retro_sscr_545, retro_sscr_934, retro_sscr_935,
Ictidomys tridecemlineatus	ENSSTOG00000004010	3 retrocopies	retro_itri_1631, retro_itri_440, retro_itri_925,
Tupaia belangeri	ENSTBEG00000001053	9 retrocopies	retro_tbel_1162, retro_tbel_1207, retro_tbel_123, retro_tbel_1394, retro_tbel_1439, retro_tbel_257, retro_tbel_2655, retro_tbel_2737, retro_tbel_513,
Xenopus tropicalis	ENSXETG00000022002	1 retrocopy	retro_xtro_18,