RetrogeneDB ID: retro_sara_353

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_176452:7236..7721(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED4
• Ensembl ID: ENSSARG00000001473
• Aliases: None
• Description: mediator complex subunit 4 [Source:HGNC Symbol;Acc:17903]

Sequence

>retro_sara_353
ATTCGACACCTACAAAAGCAGCTAAAGGAAGCAGAACAGATACTGGCAGCAGCTGTTGACCAAGCAAAAGAAAAACTCAA
ATCAATAGAAAAAGTAAGAAAGGGTGCTAGCTCCACTGAAGAAATAATTAAGTATACACATAGAATTAGTGCCACTGTGT
ATGCCCCACTGATCTGGGTTTTGGGGGACCTCGAAAACCGTACCCAACTGACTTAGTAATGCGAAGCACATTATTGGGTC
AAATGAACAATCTTCCTTCTAACGGTGTGAATGCCCACCTACCAGGACAATCACTTGTAGTGGGGAGATTGCTAGATGTC
CTTGCCCCTCAGTACCCATGGTAATCAAATGATATGTCAATTAATATGTTGCCACCAAATCACCATAATGACTACTTGTT
AGAACCTCTGGGACATGATAAAGAAAATGAAGATGATGTAGAGGTTATGTCAACAGATTCCTCAAGCAGTAGTGGCGACT
CTGAT

Alignment

ORF - retro_sara_353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.09 %
• Parental protein coverage: 60.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQQLQKQLKEAEQILXXXXXXXXXXXXXXXXXXXXAISSEEIIKYAHRISASNAVCAPLTWVPGD-PRRP
          I..LQKQLKEAEQIL....................A.S.EEIIKY.HRISA...V.APL.WV.GD.PR.P
Retrocopy IRHLQKQLKEAEQILAAAVDQAKEKLKSIEKVRKGASSTEEIIKYTHRISAT--VYAPLIWVLGD<PRKP

Parental  YPTDLEMRSGLLGQMNNPSSNGVNGHLPGDALAAGRLPDVLAPQYPWQSNDMSINMLPPSHSSDFLLEPP
          YPTDL.MRS.LLGQMNN..SNGVN.HLPG..L..GRL.DVLAPQYPW.SNDMSINMLPP.H..D.LLEP.
Retrocopy YPTDLVMRSTLLGQMNNLPSNGVNAHLPGQSLVVGRLLDVLAPQYPW*SNDMSINMLPPNHHNDYLLEPL

Parental  GHNKENEDDVEVMSTDSSSSSSDSD
          GH.KENEDDVEVMSTDSSSSS.DSD
Retrocopy GHDKENEDDVEVMSTDSSSSSGDSD

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_353 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003718	1 retrocopy	retro_amel_1882,
Canis familiaris	ENSCAFG00000004451	1 retrocopy	retro_cfam_1792,
Callithrix jacchus	ENSCJAG00000009256	1 retrocopy	retro_cjac_3937,
Dasypus novemcinctus	ENSDNOG00000018064	1 retrocopy	retro_dnov_1342,
Myotis lucifugus	ENSMLUG00000009265	1 retrocopy	retro_mluc_178,
Mustela putorius furo	ENSMPUG00000001437	1 retrocopy	retro_mputfur_162,
Mus musculus	ENSMUSG00000022109	1 retrocopy	retro_mmus_3576,
Sorex araneus	ENSSARG00000001473	1 retrocopy	retro_sara_353 ,
Tupaia belangeri	ENSTBEG00000014259	1 retrocopy	retro_tbel_292,