RetrogeneDB ID: retro_sara_407

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_195130:6352..7137(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3A3
• Ensembl ID: ENSSARG00000014204
• Aliases: None
• Description: splicing factor 3a, subunit 3, 60kDa [Source:HGNC Symbol;Acc:10767]

Sequence

>retro_sara_407
ATGGAGACAATTTTGGAAAAGAAGCAGTAATATGAGGAGAAATGGCTCATGGATGTCATGGCCAAAGATATGCTCACTAA
TAAATCCATACTCAACAACCCAATTAATTCTGACCATCACACGTTGGCCATGCATGATAGGTGTATGGAAGTCAGTGAGA
ACCGAAGGGATTTGTATGACGATAAGGGTTGACTATAAAAGGAGGAACTCAATATCATTTCAAGACCAAACAAGTTTGCT
GAATTCTACAACAAACTCAAGCAAATACAGAAATTCCATAGGAATCACCCAAATGACTTCTCTGTGGCAGTGTTGGTAGA
ATTTGAAGAACTTCTAAATGATTGAGAGAACCCAGTAAAATAGCCACAAAACTTGGTGGAATTCACAGATGAAGAGAGCT
ATGGCCATTACCTTGATCTCCATGACTTTTACCTCAAACACATTAACCTGAAGGCCTCTAAAAAGTTGGATTACATCACA
TGCTTGTCTTTCTTTGACCACCTATTTGACATCTCTGAAGAAAGGAAGAATGCAGAGTACAAGTAAAACTTAAAAATGTA
ATTTGAGTAAATTCAAGATGCTATAGAGAGAGTGAAACTCGTACAAGACCAGAATGGGCTTTTTGGAAGACTCGGACAGT
TTGAGAAGTAGGGCAATTGCACCTTCTCTCAATAGCGACAAGAAACAAGGAGTCCCTGGACTCCTGGAGCATATCGTGAC
CTCTCTGTATTCTCCTCCTAGGAGGAGCAGCCTCCCTAGGTTTGGACAGATTGAAATCTGCTCTT

Alignment

ORF - retro_sara_407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.97 %
• Parental protein coverage: 53.11 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDLYDDKD---GR
          METILE....Y..E...LMDVMAK.MLT.KS.L...INSDH.T.AM.DR.MEVS.N.RDLYDDK......
Retrocopy METILEKKQ*Y--EEKWLMDVMAKDMLTNKSILNNPINSDHHTLAMHDRCMEVSENRRDLYDDKG*L*KE

Parental  EKLVVPGPNEFAESHNRITQKKKFPRGKHPNGICVPMSVEFEELLKARENPSEEAQNLVEFTDEEGYGRY
          E......PN.FAE..N...Q..KF.R..HPN...V...VEFEELL...ENP....QNLVEFTDEE.YG.Y
Retrocopy ELNIISRPNKFAEFYNKLKQIQKFHRN-HPNDFSVAVLVEFEELLND*ENPVK*PQNLVEFTDEESYGHY

Parental  LDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNEL
          LDLHD.YLK.INLKAS.KLDYIT.LS.FD.LFDI..ERKNAEYK..L.M..E..QD...RVK..QDQN.L
Retrocopy LDLHDFYLKHINLKASKKLDYITCLSFFDHLFDISEERKNAEYK*NLKM*FE*IQDAIERVKLVQDQNGL

Parental  FGKIQTEFEKKWDNGTFPGWPKETSSALTHAGAHLDLSAFSSWEE-LASLGLDRLKSAL
          FG.....FE.K..N.TF.....ET.S..T..GA..DLS.FSS.EE..ASLGLDRLKSAL
Retrocopy FGRL-GQFE-K*GNCTFSQ*RQETRSPWT-PGAYRDLSVFSS*EE<AASLGLDRLKSAL

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_407 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001262	1 retrocopy	retro_amel_485,
Canis familiaris	ENSCAFG00000003222	1 retrocopy	retro_cfam_176,
Callithrix jacchus	ENSCJAG00000002176	1 retrocopy	retro_cjac_4109,
Cavia porcellus	ENSCPOG00000008660	1 retrocopy	retro_cpor_658,
Homo sapiens	ENSG00000183431	2 retrocopies	retro_hsap_2441, retro_hsap_937,
Macropus eugenii	ENSMEUG00000002534	3 retrocopies	retro_meug_1135, retro_meug_1346, retro_meug_642,
Macaca mulatta	ENSMMUG00000023199	1 retrocopy	retro_mmul_631,
Monodelphis domestica	ENSMODG00000017729	1 retrocopy	retro_mdom_269,
Nomascus leucogenys	ENSNLEG00000011720	1 retrocopy	retro_nleu_2775,
Pan troglodytes	ENSPTRG00000000559	2 retrocopies	retro_ptro_1411, retro_ptro_649,
Sorex araneus	ENSSARG00000014204	1 retrocopy	retro_sara_407 ,