RetrogeneDB ID: retro_sara_311

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_158488:5622..6291(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS4X
• Ensembl ID: ENSSARG00000010806
• Aliases: None
• Description: ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]

Sequence

>retro_sara_311
GAGTGTCTTCCACTGATCAGTTTCCTAAAAAACAGGCTGAAATATGCCCTAACAAGAGATGAGCTGAAGATCCGCACGCA
GCATTTCTTTAAGATAGATGAAAAACTCTGCTTCAAGATAACCTACCCTGCAGGCTTTATGAATGTCATCAGCCTTGATA
AAAGCGGAGACAATTTCCATCTGGTCTATGACACCAAAGAATGCTTTGCTATTCATTGCATCACACATCATGACCAAGTA
CAAGTTATACAAAGTGAGAAAGATCTTTGTGGACACCAGAGAAATCCCTCACTTGGTGACATGCAATGCTCTCACCATTT
GCTATCCTGACCCCCTCATCAACATGAACAACACCATTCAGATTGATTTGGGAACCCCAAAATTTACTGATTTCATCAAG
TTTGACACTGGAAATCTATGCATGGTGACCTGTGGTGCTAACCTGAGAAGAATTTGTGTGATCACCAACAGGGGAAAGAC
ATCCCAGTTCTTTTGATGTTGTCCAAGTGAAAGATGCCAATGGCAAAATCTTTGCCACCCACCTCTCCAATATTTTTGTG
ATTGGCAAAGGCAACAAACCATGGATTTCTCTCCCCACAAGGAAAAGACATTCATGTCACCATTGCTGAAGAAAGAGACA
AAAGACTGGTTGTCAAACAGAGCAATGGC

Alignment

ORF - retro_sara_311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.72 %
• Parental protein coverage: 94.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRF
          ECLPLI.FL.NRLKYALT.DE.K.I..Q.F.KID.K....ITYPAGFM.VIS.DK.G.NF.L.YDTK..F
Retrocopy ECLPLISFLKNRLKYALTRDELK-IRTQHFFKIDEKLCFKITYPAGFMNVISLDKSGDNFHLVYDTKECF

Parental  AVHRITPEEAKYKLCKVRKIFVGTKGIP-HLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTG
          A.H.IT............K...G....P.HLVT..A.TI.YPDPLI..N.TIQIDL.T.K.TDFIKFDTG
Retrocopy AIHCITHHD-QVQVIQSEKDLCGHQRNP>HLVTCNALTICYPDPLINMNNTIQIDLGTPKFTDFIKFDTG

Parental  NLCMVTGGANLGRIGVITNR-ERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISL-PRGKSIRL
          NLCMVT.GANL.RI.VITNR.ERHP.SFDVV.VKDANG..FAT.LSNIFVIGKGNKPWISL.P.GK.I..
Retrocopy NLCMVTCGANLRRICVITNR>ERHPSSFDVVQVKDANGKIFATHLSNIFVIGKGNKPWISL>PQGKDIHV

Parental  TIAEERDKRLAAKQSSG
          TIAEERDKRL..KQS.G
Retrocopy TIAEERDKRLVVKQSNG

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_311 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 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,
Sorex araneus	ENSSARG00000010806	6 retrocopies	retro_sara_202, retro_sara_245, retro_sara_297, retro_sara_311 , retro_sara_321, retro_sara_612,