RetrogeneDB ID: retro_sara_413

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_195792:4885..5521(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS2
• Ensembl ID: ENSSARG00000001275
• Aliases: None
• Description: HAUS augmin-like complex, subunit 2 [Source:HGNC Symbol;Acc:25530]

Sequence

>retro_sara_413
ATGGCTGGTGGGAAGCCCTGGGAGCTGGTCTTGGGACCAAATGCAGCTGGGATGTTGTTGAGCCATTTCAGGGCTTTGGG
GACTGTCACTTAGGAGATGTTAGATATAGCTAAGAAACCAGTTTCTTGCTTTGAGAACTTCTCCAAACAACAGCAAATTG
CAGATATTAAAGCTGAAATTGACCAGAAAGACCTAGAAATTGAACTATCAAGACCATAAAAAGATTCCATAGATGTTGTT
CATCCTTCTTTTTTAGCTCAGAAGTGTCAGAGTTTGCAAAGCATGAATAATCATCTGGAAGCAATTCTGAAAGAAAAGCA
GTCTCTCGGGCAAAGACTGTTAAAACCCATGTGTCAGGAAAACTTGCCCATTGAAGCTGTTTATCACAGATACACGGTCC
ATTTGTTGGAGTTGGCAGTGACTTTCGTCGAAAGATTAGAATCCAATCTTGAAACTATTAGAGATATCCCTCATTTAGAT
GAAATTTTTTAAAAAATGAGCAATTCTTTAGCAAAAACGAATATTTTGGTGACTAAGACAGAAGAACTGGTAGAGAGTGT
ACTTAAATGGCGACAACAACAAAAGGAAATTTCTTCTTGAATTTCAAACATATTAACTAAAGAAAGTAACTCTCAT

Alignment

ORF - retro_sara_413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.96 %
• Parental protein coverage: 90.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGAKPWEPVSETNAAGMLLSHFRASGTVTQEMLDIAKKPVSCFENFSRQQQIADIRAEIDQKDLEIELL
          MAG.KPWE.V...NAAGMLLSHFRA.GTVT.EMLDIAKKPVSCFENFS.QQQIADI.AEIDQKDLEIEL.
Retrocopy MAGGKPWELVLGPNAAGMLLSHFRALGTVT*EMLDIAKKPVSCFENFSKQQQIADIKAEIDQKDLEIELS

Parental  RLEKDSIDVVHPSFLAQKCQS-QGMNNHLEAILKEKRSLRQRLLKPRCQENLPIEAVYHRYMVHLLELAV
          R..KDSIDVVHPSFLAQKCQS.Q.MNNHLEAILKEK.SL.QRLLKP.CQENLPIEAVYHRY.VHLLELAV
Retrocopy RP*KDSIDVVHPSFLAQKCQSLQSMNNHLEAILKEKQSLGQRLLKPMCQENLPIEAVYHRYTVHLLELAV

Parental  TFIEKLESNLETIRNIPHLDENLKKMSKSLAKTNILVTKTEELAENILKWREQQKEISSCIPNIFTKESH
          TF.E.LESNLETIR.IPHLDE...KMS.SLAKTNILVTKTEEL.E..LKWR.QQKEISS.I.NI.TKES.
Retrocopy TFVERLESNLETIRDIPHLDEIF*KMSNSLAKTNILVTKTEELVESVLKWRQQQKEISS*ISNILTKESN

Parental  LH
          .H
Retrocopy SH

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_413 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003587	4 retrocopies	retro_meug_1171, retro_meug_1231, retro_meug_702, retro_meug_996,
Microcebus murinus	ENSMICG00000000819	1 retrocopy	retro_mmur_648,
Monodelphis domestica	ENSMODG00000017882	1 retrocopy	retro_mdom_1473,
Oryctolagus cuniculus	ENSOCUG00000011004	1 retrocopy	retro_ocun_1322,
Sorex araneus	ENSSARG00000001275	2 retrocopies	retro_sara_123, retro_sara_413 ,
Ictidomys tridecemlineatus	ENSSTOG00000006207	1 retrocopy	retro_itri_618,
Vicugna pacos	ENSVPAG00000006260	1 retrocopy	retro_vpac_599,