RetrogeneDB ID: retro_sscr_897

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:22043437..22043812(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKIRIN2
• Ensembl ID: ENSSSCG00000004307
• Aliases: None
• Description: akirin 2 [Source:HGNC Symbol;Acc:21407]

Sequence

>retro_sscr_897
AAACAACATATGCACAACATAAAACAAGAGTGTAAGTGCATGCAGAAGAAAAGACATTTAGAAACGAGTTTCCAACAGTC
GGATCCATGCTGTACTTCTGAAGCGCAGCCACATGCAGTTCTCCTCAGTGGACCAGCTTCACCAGGGGTTCCATCAGCAA
CATCCTCACCATTAAAAAAAGAACAGCCCTTATTCACTCTACAGCAGGTTGGGATGATCTGTGAACATTTATTGAAAGAA
CGTGAAGAGAAAGTTCGAGAAAAGTATGAGGAAATATTAAACACAAAACGTGCAGAACAGTATGATGCATTTGTGAAGTT
TACGCATGATCAAATATTGTGATGCTATGGAGAGCAGCCTGCTAGTTATGTTTCA

Alignment

ORF - retro_sscr_897 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.6 %
• Parental protein coverage: 61.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQILYNIKQEYKRMQKRRHLETSFQQTDPCCTSDAQPHAFLLSGPASPGTPSATSSPLKKEQPLFTLRQV
          .Q...NIKQE.K.MQK.RHLETSFQQ.DPCCTS.AQPHA.LLSGPASPG.PSATSSPLKKEQPLFTL.QV
Retrocopy KQHMHNIKQECKCMQKKRHLETSFQQSDPCCTSEAQPHAVLLSGPASPGVPSATSSPLKKEQPLFTLQQV

Parental  GMICERLLKEREEKVREEYEEILNTKLAEQYDAFVKFTHDQIMRRYGEQPASYVS
          GMICE.LLKEREEKVRE.YEEILNTK.AEQYDAFVKFTHDQI...YGEQPASYVS
Retrocopy GMICEHLLKEREEKVREKYEEILNTKRAEQYDAFVKFTHDQIL*CYGEQPASYVS

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	73.80 RPM
SRP014902_testis	0.14 RPM	53.18 RPM
SRP018288_heart	0.00 RPM	24.70 RPM
SRP018288_kidney	0.00 RPM	47.28 RPM
SRP018288_liver	0.00 RPM	36.62 RPM
SRP018288_lung	0.00 RPM	70.16 RPM
SRP018856_adipose	0.15 RPM	42.73 RPM
SRP035408_brain	0.00 RPM	81.15 RPM
SRP035408_liver	0.00 RPM	32.85 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_897 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_897 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_897 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003082	1 retrocopy	retro_cfam_1014,
Choloepus hoffmanni	ENSCHOG00000012160	1 retrocopy	retro_chof_413,
Callithrix jacchus	ENSCJAG00000000769	1 retrocopy	retro_cjac_2231,
Dasypus novemcinctus	ENSDNOG00000000549	1 retrocopy	retro_dnov_1788,
Homo sapiens	ENSG00000135334	1 retrocopy	retro_hsap_2991,
Gorilla gorilla	ENSGGOG00000002448	1 retrocopy	retro_ggor_2071,
Macaca mulatta	ENSMMUG00000002824	1 retrocopy	retro_mmul_1914,
Pongo abelii	ENSPPYG00000016831	1 retrocopy	retro_pabe_2477,
Pan troglodytes	ENSPTRG00000018409	1 retrocopy	retro_ptro_2023,
Rattus norvegicus	ENSRNOG00000008288	1 retrocopy	retro_rnor_1499,
Sorex araneus	ENSSARG00000006084	1 retrocopy	retro_sara_701,
Sarcophilus harrisii	ENSSHAG00000011555	2 retrocopies	retro_shar_363, retro_shar_579,
Sus scrofa	ENSSSCG00000004307	1 retrocopy	retro_sscr_897 ,