RetrogeneDB ID: retro_sara_495

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_227143:4799..5262(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED6
• Ensembl ID: ENSSARG00000002553
• Aliases: None
• Description: mediator complex subunit 6 [Source:HGNC Symbol;Acc:19970]

Sequence

>retro_sara_495
AATCTGCTGGGAATCTTTTGGGTTGACAGTGCACGGATCCCTATTTTGAACAGGGGAAGTGTCTTGGATTACTTTTCAGA
AAGAAGTAATCCATTTTTGACAGGACGTGTAAAATGAGTGGTCAAAATGCACGGGCTAATGTTAGAACACTTAAATCAAG
TGGTTGGAGTGGAGTACCTCCTTTCACGTGCTCAAGAACCCATTCTTTTTATAATTCGGAAACAACAGCGACAATCTCCT
ACCCAAGTTGTTCCAATGGCTGATTACTACATCATTGCTGGAGTAATCTATCATGCACCAGACTTGGGATAAGTTACAAA
CTCTAGAGTGCTCATTGCAGTACATGGAATTCAGTCAGCTTTTGATAAAGCTAGGTCATACTGTCGATACCATCTTTTCA
AAGGGTATTTGGTGGCACTTCAAAGATCATGAGGAGCAAGATAAAGTTAAACCTAAAGCCAAA

Alignment

ORF - retro_sara_495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.91 %
• Parental protein coverage: 65.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NLLGISWVDSAWIPILNSGSVLDYFSERSNPF-YDRTCN-NE-VVKMQRLTLEHLNQMVGVEYILLHAQE
          NLLGI.WVDSA.IPILN.GSVLDYFSERSNPF..DRTC..NE.VVKM..L.LEHLNQ.VGVEY.L..AQE
Retrocopy NLLGIFWVDSARIPILNRGSVLDYFSERSNPF<FDRTCK<NE<VVKMHGLMLEHLNQVVGVEYLLSRAQE

Parental  PILFIIRKQQRQSPTQVVPMADYYIIAGVIYQAPDLGSVINSRVLTAVHGIQSAFDEAMSYCRYHPSKGY
          PILFIIRKQQRQSPTQVVPMADYYIIAGVIY.APDLG.V.NSRVL.AVHGIQSAFD.A.SYCRYH..KGY
Retrocopy PILFIIRKQQRQSPTQVVPMADYYIIAGVIYHAPDLG*VTNSRVLIAVHGIQSAFDKARSYCRYHLFKGY

Parental  -WWHFKDHEEQDKVKPKAK
          .WWHFKDHEEQDKVKPKAK
Retrocopy >WWHFKDHEEQDKVKPKAK

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_495 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013091	1 retrocopy	retro_fcat_1612,
Myotis lucifugus	ENSMLUG00000017357	1 retrocopy	retro_mluc_265,
Monodelphis domestica	ENSMODG00000007174	3 retrocopies	retro_mdom_1190, retro_mdom_524, retro_mdom_625,
Otolemur garnettii	ENSOGAG00000001311	1 retrocopy	retro_ogar_2597,
Ochotona princeps	ENSOPRG00000008957	1 retrocopy	retro_opri_820,
Sorex araneus	ENSSARG00000002553	1 retrocopy	retro_sara_495 ,
Tupaia belangeri	ENSTBEG00000002302	1 retrocopy	retro_tbel_2272,