RetrogeneDB ID: retro_sscr_545

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:34943549..34943866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2A2
• Ensembl ID: ENSSSCG00000004583
• Aliases: None
• Description: general transcription factor IIA, 2, 12kDa [Source:HGNC Symbol;Acc:4647]

Sequence

>retro_sscr_545
TCATATCAGTTATACAGAACTACTACTGTGGGAAAGAGTCTTCAGGAAAGCCTCGATGAACTTACACAGTCTCAGGAGAT
TACCCCACAACCTGCCCTATAAGTTCTACTTCCGTTTGATAAGGCTATAAATTCAGCCTTGGCACAGAGAGTCAGGAACA
GAGTCAACTTTAGAGGCTTTCTAAATATGTACAGATTCTGCAATAATGTGTGGACTTTTATACTGAATGATGTTGAATTC
AGAGAGGTGACATTAAAGTGGACAAAGTGAAAATTGTAGCCTGTAATGCTAAAAATACTAGTTCCAATACTACAGAA

Alignment

ORF - retro_sscr_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.98 %
• Parental protein coverage: 99.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINSALAQRVRNRVNFRGSLNTYRFCDNV
          .YQLYR.TT.G.SLQESLDEL.QSQ.ITPQ.AL.VLL.FDKAINSALAQRVRNRVNFRG.LN.YRFC.NV
Retrocopy SYQLYRTTTVGKSLQESLDELTQSQEITPQPAL*VLLPFDKAINSALAQRVRNRVNFRGFLNMYRFCNNV

Parental  WTFVLNDVEFREVTELIKVDKVKI-VACDGKNTGSNTTE
          WTF.LNDVEFREVT...K..K.K..VAC..KNT.SNTTE
Retrocopy WTFILNDVEFREVT--LKWTK*KL<VACNAKNTSSNTTE

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
SRP014902_placenta	0.00 RPM	3.19 RPM
SRP014902_testis	0.14 RPM	9.76 RPM
SRP018288_heart	0.03 RPM	26.27 RPM
SRP018288_kidney	0.10 RPM	24.13 RPM
SRP018288_liver	0.00 RPM	13.27 RPM
SRP018288_lung	0.00 RPM	11.61 RPM
SRP018856_adipose	0.00 RPM	3.19 RPM
SRP035408_brain	0.00 RPM	22.68 RPM
SRP035408_liver	0.00 RPM	19.67 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_545 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_545 has 0 orthologous retrocopies within eutheria group .

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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,