RetrogeneDB ID: retro_sara_169

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_5573:21191..21962(-)
• Located in intron of: ENSSARG00000004461

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSARG00000000397
• Aliases: None
• Description: None

Sequence

>retro_sara_169
ATGAGTTTTAGTATGAGTTCTTCTAGAGGGCCACTTCCACGCTGTAAAAGAGGACCACCACCACGAAGTGGGGGACCACC
TCCTAAAAGGTCTGCCCCCTCAGGACCAGTTCGAAGCAGTAGTGGAATGGGAGGAAGAGCTCCTGTATCCCGTGGAAGAG
ACAGTTATGGAGGCCCACCTCGTAGGGAACCCCTACCTTCTCGAAGAGATGTTTATTTGTCCCCAAGAGATGATGGATAT
TCTACTAAAGATAGCTACTCGAGCAGAGATTACCCAAGTTCACGGGATACCAGAGATTATGCACCACCCCCGAGAGATTA
CACCTACCGTGATTATGGGCATTCCAGTTCACGTGATGACTATCCATCAAGAGGGTATAGTGATCGAGATGGCTATGGTC
GGGATCGAGACTATTCAGATCATCCCAGTGGAGGCTCCTACAGAGATTCCTATGAGAGTTATGGTAATTCACGTAGTGCT
CCACCTACGCGAGGGCCACCACCATCTTATGGTGGAAGCAGTCGCTATGATGATTACAGCAGCTCACGGGATGGATATGG
TGGAAGCCGAGACAGTTACTCAAGCAGCCGAAGTGATCTCTACTCAAGTGGTCGTGATCGGGTTGGCAGACAAGACAGAG
GGCTACCGCCTTCTATGGAAAGGGGGTACCCTCCTCCACGCGATTCCTACAGCAGTTCAAGCCGTGGAGCACCAAGAGGT
GGTGGTCGTGGAGGAAGTCGATCTGATAGATGGGGATGCAGAAGCAGATAT

Alignment

ORF - retro_sara_169 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.28 %
• Parental protein coverage: 80.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNFNMSSSRGPLP-VKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRD
          M.F.MSSSRGPLP..KRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRD
Retrocopy MSFSMSSSRGPLPRCKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRD

Parental  VYLSPRDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSD
          VYLSPRDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSD
Retrocopy VYLSPRDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSD

Parental  HPSG-SYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGR
          HPSG.SYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGR
Retrocopy HPSGGSYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGR

Parental  QDRGLPPSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY
          QDRGLPPSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDR.G.RSRY
Retrocopy QDRGLPPSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDRWGCRSRY

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_169 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 21 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Dipodomys ordii	ENSDORG00000015481	1 retrocopy	retro_dord_793,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus	ENSMICG00000006856	2 retrocopies	retro_mmur_1252, retro_mmur_661,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Ochotona princeps	ENSOPRG00000016593	1 retrocopy	retro_opri_372,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Sorex araneus	ENSSARG00000000397	1 retrocopy	retro_sara_169 ,
Sorex araneus	ENSSARG00000012900	1 retrocopy	retro_sara_467,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,