RetrogeneDB ID: retro_sara_732

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_42123:514..1223(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTA2
• Ensembl ID: ENSSARG00000005778
• Aliases: None
• Description: actin, alpha 2, smooth muscle, aorta [Source:HGNC Symbol;Acc:130]

Sequence

>retro_sara_732
GCTGTGCTGTCCCTGGATTCCTCTGGCTGCGTCATGGGTACGGAAACAGACTCCGGTGACGGGGTGCCCCACACGGTGCC
CACCTAGGATGAGGGCTACGCACTGCCCCCTACCATCCTGGGTCTGAACTTGGCCAGCCGCCACCTGACCGACGACCTCA
TCACGGTCCTCATGGGGCACAGCTTCAGCCTCACCACCTCGGCTGAGTGGGAGATCATGGGCGACATCAAGGAGAACTTG
TGCTACGTGGCGCTGGACTTTGAGTGGGAGATGGCCACGGCGGCCTCCTTGTCCTCCCTGGAGGAGAGCTGCTCACAGCC
AGGTGATCACCATCAGCCATGAGCGCTTCTGCTGCCCGAGATGCTGTTTCCGCTCTCCTTTCTGGGCAAGGAGTCCTGTG
GCATCCATGAGACGGCCCTTCAGTTCCATCATAAACTGTGACATGGACATGCGGAAGGCCCCTGTGTGCTGAAAACGGTG
CCCTCTGGCAGCACCAGCATGTACTCCGGCGTTGCCTACAGGATGCAGAAGGAGACCATTGCCCTGGCCCCCGCACCATG
AAGATCAAGATCATGGCGCCTCTGGAGCACAAGTACTCGGTGTGGATGGGGCCTCCACCCCGGCCTCGCTGTCCACCCTC
CAGGAGATGTGGATCAGCAAGCAGGGGTATGATGAGTCTGGCTCGTCCATCGTCCACCACAAAGGCTTC

Alignment

ORF - retro_sara_732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.35 %
• Parental protein coverage: 63.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  AVLSLYASGRTTGIVLDSGDGVTHNVPI-YEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAER
          AVLSL..SG...G...DSGDGV.H.VP...EGYALP..I..L.LA.R.LTD.L...L.....S..T.AE.
Retrocopy AVLSLDSSGCVMGTETDSGDGVPHTVPT*DEGYALPPTILGLNLASRHLTDDLITVLMGHSFSLTTSAEW

Parental  EIVRDIKEKLCYVALDFENEMATAASSSSLEKSYE-LPDGQVITIGNERFRCP-ETLFQPSFIGMESAGI
          EI..DIKE.LCYVALDFE.EM...A...SL....E.....QVITI..ERF.CP.E.LF..SF.G.ES.GI
Retrocopy EIMGDIKENLCYVALDFEWEM---ATAASLSSLEE>AAHSQVITISHERFCCP<EMLFPLSFLGKESCGI

Parental  HETT-YNSIMKCDIDIRK-DLYANN-VLSGGTTMYPGIADRMQKEITALAPS-TMKIKIIAPPERKYSVW
          HET....SI..CD.D.RK..L.A.N.V.SG.T.MY.G.A.RMQKE..ALAP..TMKIKI.AP.E.KYSVW
Retrocopy HETA>FSSIINCDMDMRK>PLCAEN>VPSGSTSMYSGVAYRMQKETIALAPA<TMKIKIMAPLEHKYSVW

Parental  IG-GSILASLSTFQQMWISKQEYDEAGPSIVHRKCF
          .G..S..ASLST.Q.MWISKQ.YDE.G.SIVH.K.F
Retrocopy MG<ASTPASLSTLQEMWISKQGYDESGSSIVHHKGF

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_732 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 13 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000759	3 retrocopies	retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus	ENSDNOG00000006719	1 retrocopy	retro_dnov_32,
Echinops telfairi	ENSETEG00000008526	1 retrocopy	retro_etel_41,
Macropus eugenii	ENSMEUG00000010843	1 retrocopy	retro_meug_1374,
Myotis lucifugus	ENSMLUG00000015509	3 retrocopies	retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Sorex araneus	ENSSARG00000005778	1 retrocopy	retro_sara_732 ,
Sorex araneus	ENSSARG00000012197	1 retrocopy	retro_sara_267,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta	ENSTSYG00000008155	5 retrocopies	retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos	ENSVPAG00000010621	3 retrocopies	retro_vpac_12, retro_vpac_355, retro_vpac_651,