RetrogeneDB ID: retro_sara_414

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_196340:6470..6881(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000013200
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PCBP3
• Ensembl ID: ENSSARG00000007629
• Aliases: None
• Description: poly(rC) binding protein 3 [Source:HGNC Symbol;Acc:8651]

Sequence

>retro_sara_414
AAAGGGGAGTCGGTTAAGAGGATCCGCGAGGAGAGTGGCGCGCGGATCAACATCTCGGAGGGGAATTGCCCGGAGAGAAT
CATCACTCTGACCGGCCCCACCAATGCCATCTTTAAGGCCTTCGCGATGATCATCGACAAGCTGGAGGAAGATATCAACA
GCTCCATGACCAACAGCACGGCGGCCAGCCGGCCCCCGGTCACCCTGAGGCTCGTGGTGCCGGCCACCCAGTGCGGCTCC
CTGATCGGGAAAGGCGGCTGTAAGATCAAAGAGATCCGCGAGAGCACGGGCGCCCAGGTGCAGGTGGCGGGGGATATGCT
GCCCAACTCCACCGAGCGGGCCATCACCATCGCGGGCGTGCCGCAGTCGGTCACCGAGTGTGTCAAGCAGATCTGCCTGG
TCATGCTGGAG

Alignment

ORF - retro_sara_414 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.18 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGETVKKMREESGARINISEGNCPERIVTITGPTDAIFKAFAMIAYKFEEXXXXXXXXXXXTSKPPVTLR
          KGE.VK..REESGARINISEGNCPERI.T.TGPT.AIFKAFAMI..K.EE............S.PPVTLR
Retrocopy KGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMIIDKLEEDINSSMTNSTAASRPPVTLR

Parental  LVVPASQCGS-IGKGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLE
          LVVPA.QCGS.IGKGG.KIKEIRESTGAQVQVAGDMLPNSTERA.TI.G.P.....CVKQIC.VMLE
Retrocopy LVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGVPQSVTECVKQICLVMLE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_414 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003648	1 retrocopy	retro_cpor_257,
Dipodomys ordii	ENSDORG00000003640	2 retrocopies	retro_dord_742, retro_dord_748,
Myotis lucifugus	ENSMLUG00000003074	1 retrocopy	retro_mluc_574,
Nomascus leucogenys	ENSNLEG00000002639	1 retrocopy	retro_nleu_2044,
Oryctolagus cuniculus	ENSOCUG00000002696	1 retrocopy	retro_ocun_1257,
Rattus norvegicus	ENSRNOG00000001245	1 retrocopy	retro_rnor_2656,
Sorex araneus	ENSSARG00000007629	1 retrocopy	retro_sara_414 ,
Tursiops truncatus	ENSTTRG00000015075	1 retrocopy	retro_ttru_1095,