RetrogeneDB ID: retro_sara_288

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_148284:4350..4654(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HPRT1
• Ensembl ID: ENSSARG00000008045
• Aliases: None
• Description: hypoxanthine phosphoribosyltransferase 1 [Source:HGNC Symbol;Acc:5157]

Sequence

>retro_sara_288
AATGACCAGTTAACTGGAGTCACCAATGGAGATAATTTATCAACTTTAACTGGAAAGAAGGTCTTTATATGGAAGACATC
TTTGACACTGGCAAAACAAAGCAAACTTTGCTGTCCTTGTCAAGCAGCATAATCCCAAGATGGTCAAGCTTGCAAGTTTA
TTGGTGAAAAAGACCCCTCACAGCATTGAATATAGACCAGACTTTGTTGGATTTGAAATTCTAGACAAGTTTGTCCTTGA
CTATAATGAATACTTCAGGAACTTGACCCATGTCAGCAGCAAAAACAGAAAGGCCAAATACAAA

Alignment

ORF - retro_sara_288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.57 %
• Parental protein coverage: 99.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NDQSTGDIKVIGGDDLSTLTGKNVLI-VEDIIDTGKTMQTLLS-LVKQHNPKMVKVASLLVKRTPRSVGY
          NDQ.TG...V..GD.LSTLTGK.V.I..EDI.DTGKT.QTLLS.LVKQHNPKMVK.ASLLVK.TP.S..Y
Retrocopy NDQLTG---VTNGDNLSTLTGKKVFI<MEDIFDTGKTKQTLLS<LVKQHNPKMVKLASLLVKKTPHSIEY

Parental  RPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISENGKAKYK
          RPDFVGFEI.DKFV....LDYNEYFR.L.HV...S.N.KAKYK
Retrocopy RPDFVGFEILDKFV----LDYNEYFRNLTHVS--SKNRKAKYK

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_288 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001339	1 retrocopy	retro_amel_129,
Bos taurus	ENSBTAG00000014685	3 retrocopies	retro_btau_162, retro_btau_179, retro_btau_721,
Felis catus	ENSFCAG00000004575	2 retrocopies	retro_fcat_104, retro_fcat_1608,
Rattus norvegicus	ENSRNOG00000031367	2 retrocopies	retro_rnor_1208, retro_rnor_2491,
Sorex araneus	ENSSARG00000008045	1 retrocopy	retro_sara_288 ,
Sarcophilus harrisii	ENSSHAG00000007965	3 retrocopies	retro_shar_470, retro_shar_513, retro_shar_661,