RetrogeneDB ID: retro_sara_593

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_236359:92846..93469(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNPDA2
• Ensembl ID: ENSSARG00000004814
• Aliases: None
• Description: glucosamine-6-phosphate deaminase 2 [Source:HGNC Symbol;Acc:21526]

Sequence

>retro_sara_593
AGTACACCTTTATTGTGTTATAAAACACTAATAGAATTTCATAAGAATGGAGACCTCTCATTTAAATATGTGAAAACCTT
TAACATGGATGAATATGTAGGACTTCTCAGAAATCATCCTGAAAGCTACCGTTCATACATGTGGAATAACTTTTTAAAGC
ATGTTAATATGATCCCAATAATGCTCATATACTTGATGGGAATGCAACAGATTTACAAGCAGAATGTGATGCTTTTGGAA
AAAAAATAAAAGAAGTTGGAGGAATTGATCTTTTTGTTGAAGGAATAGGTCCAGATGGTCATATCACTTTCAATGAGCAA
GGATTAAATTTAGTTTCAAGGACAAGATTAAAAACTCTAGCAATGGACACAATGGACACCATTTTGACCAATGCAAAATA
TTTTGATGGAGATTTGTCAAAGGTGCCAGCTATGGCTCTAGCAGTTGGTGTGGGGACAGTAATGGATGCCAGAGAAGTTA
CGATCCTCATAACAGGTGCACATAAGGCATTTGCCCTGTACAAAGCAACTGAAGAAGGAGTCAATCACATATGGACTGTT
TCCGCTTTTCAGCAGCATCCCCAAACCATTTCTGTGTGTGACGAAGATGCCACCTTAGAATTG

Alignment

ORF - retro_sara_593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.65 %
• Parental protein coverage: 87.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STPLGCYKKLIEFHKNGDLSFKYVKTFNMDEYVGLPRNHPESYHSYMWNNFFKHVDI-DPNNAHILDGNA
          STPL.CYK.LIEFHKNGDLSFKYVKTFNMDEYVGL.RNHPESY.SYMWNNF.KHV...DPNNAHILDGNA
Retrocopy STPLLCYKTLIEFHKNGDLSFKYVKTFNMDEYVGLLRNHPESYRSYMWNNFLKHVNM<DPNNAHILDGNA

Parental  TDLQAECDAFEKKIKEAGGIDLFVGGIGPDGHIAFNEPGSSLVSRTRLKTLA---MDTILANAKYFDGDL
          TDLQAECDAF.....E.GGIDLFV.GIGPDGHI.FNE.G..LVSRTRLKTLA...MDTIL.NAKYFDGDL
Retrocopy TDLQAECDAFXXXXXEVGGIDLFVEGIGPDGHITFNEQGLNLVSRTRLKTLAMDTMDTILTNAKYFDGDL

Parental  SKVPTMALTVGVGTVMDAREVMILITGAHKAFALYKAIEEGVNHMWTVSAFQQHPRTIFVCDEDATLEL
          SKVP.MAL.VGVGTVMDAREV.ILITGAHKAFALYKA.EEGVNH.WTVSAFQQHP.TI.VCDEDATLEL
Retrocopy SKVPAMALAVGVGTVMDAREVTILITGAHKAFALYKATEEGVNHIWTVSAFQQHPQTISVCDEDATLEL

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_593 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000015385	1 retrocopy	retro_meug_1772,
Monodelphis domestica	ENSMODG00000020593	1 retrocopy	retro_mdom_67,
Sorex araneus	ENSSARG00000004814	1 retrocopy	retro_sara_593 ,
Tarsius syrichta	ENSTSYG00000010930	1 retrocopy	retro_tsyr_806,
Vicugna pacos	ENSVPAG00000011080	1 retrocopy	retro_vpac_409,