RetrogeneDB ID: retro_sara_692

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_259230:48418..48989(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3A
• Ensembl ID: ENSSARG00000001186
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) alpha [Source:HGNC Symbol;Acc:5384]

Sequence

>retro_sara_692
CACCCTTCTATGAATTTGCTGCTGCAGAAGATATTTGACCTGTATGCAAACGTCCGGCCCTGCGTCTCCATTGAAGGCTA
CAAGACCCCTTACACTGACGTGAACGTGTCACCATCCGGGAGAGCACATAGGGGGAATACAGCGGCATCGAGCACGTGAT
CGTGGACGGTGTTGTGCAGAGCATCAAGCTTATCACCGAGGAGGCCAGCAAGTGCATCACTGAGTTCGCCTTTGAGTACA
CCCGGAACAACCGTCGGAGCAAGGTCACTGCTGTGCACGAGGCCAACATCATGCGAATGTCAGATGGGCTTTTTCTGCAG
AGAGCAGAGAGGTTGCAGAAAACTGTAAAGACATAAAGTTTCATGAGCTGTACCTAGATACAGTGTGTTTGAACATGGTG
CAGGACCCATCCCAGTTCCATGTGCTGGTGATGCCGAACCTCTACGGCGACATTCTCAGGGACCTGTGTGCCGGACTGAT
AGGAGGACTGGGAGTGACGCCCAGCGGCCACACTGGCGCCATCTTTGAGTCGGTCCACGGCACTGCCCCCGATATCGCGG
GCAAGGACATG

Alignment

ORF - retro_sara_692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.8 %
• Parental protein coverage: 53.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTDVNI-VTIRENTEGEYSGIEHIIVDGVVQSIKLITEEA
          HPSMNLLL.K.FDLYANVRPCVSIEGYKTPYTDVN..VTIRE.T.GEYSGIEH.IVDGVVQSIKLITEEA
Retrocopy HPSMNLLLQKIFDLYANVRPCVSIEGYKTPYTDVNV<VTIREST*GEYSGIEHVIVDGVVQSIKLITEEA

Parental  SKRIAEFAFEYARNNHRSNVTAVHKANIMRMSDGLFLQKC-REVAENCKDIKFNEMYLDTVCLNMVQDPS
          SK.I.EFAFEY.RNN.RS.VTAVH.ANIMRMSDGLFLQ...REVAENCKDIKF.E.YLDTVCLNMVQDPS
Retrocopy SKCITEFAFEYTRNNRRSKVTAVHEANIMRMSDGLFLQRA<REVAENCKDIKFHELYLDTVCLNMVQDPS

Parental  QFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGANGVAIFESVHGTAPDIAGKDM
          QF.VLVMPNLYGDIL.DLCAGLIGGLGVTPSG..GA....IFESVHGTAPDIAGKDM
Retrocopy QFHVLVMPNLYGDILRDLCAGLIGGLGVTPSGHTGA----IFESVHGTAPDIAGKDM

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_692 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000009646	1 retrocopy	retro_meug_1784,
Macaca mulatta	ENSMMUG00000011838	1 retrocopy	retro_mmul_388,
Sorex araneus	ENSSARG00000001186	1 retrocopy	retro_sara_692 ,
Sarcophilus harrisii	ENSSHAG00000017922	1 retrocopy	retro_shar_410,