RetrogeneDB ID:

retro_sara_605

Retrocopy
location
Organism:Shrew (Sorex araneus)
Coordinates:scaffold_237465:125498..126622(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF4A1
Ensembl ID:ENSSARG00000006017
Aliases:None
Description:eukaryotic translation initiation factor 4A1 [Source:HGNC Symbol;Acc:3282]


Retrocopy-Parental alignment summary:






>retro_sara_605
GACGTGACCCTTACATTCAATACCACGGGTCTGGGGGAGGACCTGCTGTGAGGCATCTACGCCTATGGTTTTGAGAAGCC
ATCTGCTGTCCAGCAGTGAGCCATCAAGCAGATCATCAAAGGCAGAGACATCATCATGCAGTCTCAGCCTGGTACTGGCA
AGGCAGCCACCTTTAGTGTCTCAGTGCTCCAGTGCCTGGACATTCAGGTCTGTGAGACATAGGCTCTGATCTTGGCTCTG
ACGAGAGAGTTGGCTGTGCAGATCAAGAAGGGCTTGCTCACTCTGGGCAACTACGTGAATGTCCAGTGCCATGCCTGCAT
CGGGGGCACCAACGTGGGAGAGGACATCCAGAAGCTGGACTACAGGCAGCACGTGGTGGCTGGCACACCAAGATATGATA
TGATCCGGCGCAGAAGCCTGAGGACCCGCGCCATCAAGATGCTGATTTGGGATGAAGCTGATGAAATGTTGAATAAAGGC
TTCATAGAGCTAATCTACAACGTGCACCTCTACCTGCCTCCAGCCACGTAGGTGGTGCTCATCAGTGCCATGCTGCCCCA
CAAGATCCTGGAGATGACCAAAAAGTTCATGACCGACCCCATCCACATCCGGTGATGCGTGATGAGCTGATCCTGGAGGG
CATCAAGCAGTTCTTCGTGGTACTGGAGTGAGAGGAGTGGAAGTTTGACAGGCCATGTGACCTGTACGACACGCTCACCA
TCACGCAGGCCATCATCTTCTGCAACACTAAGCGGAAGGTGGACTGGCTGCCAGAGAAGATATGCAAGGCCAACTTCACC
GTGTTGTGCATGCACAGAGACATGCCGCAGAAGGAGTGTCAGTCCATCATGAAGGAGTTTCGCTCAGGCGCAGCAGCGTG
CTCATCTCTACACACGTTTGGGCCCGGGGCCTGGACGTCCCCCAGGTGTCCCTCATCGTCACCTATGACCTGCCCAACAA
CCGGTAGCTGTACACCCACAGAATCGGGAAGTCAGGTCGCTATGTCCCGCAAAGGTATGGCCATCAACTTCGTGTAGAAC
AACGACATCTGCATCCACAGGGACATCAAGCAGTACTACTCCACCCAGATCGACGAGATGCCCATGAACGTTGTCTATCT
CATC

ORF - retro_sara_605 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.64 %
Parental protein coverage: 93.1 %
Number of stop codons detected: 7
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL
.....F....L.E.LL.GIYAYGFEKPSA.QQ.AI...IKG.D.I.Q.Q.GTGK.ATF..S.LQ......
RetrocopyDVTLTFNTTGLGEDLL*GIYAYGFEKPSAVQQ*AIKQIIKGRDIIMQSQPGTGKAATFSVSVLQCLDIQV
ParentalKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR
..T.AL.LA.TRELA.QI.K....LG.Y....CHACIGGTNV....QKL.....H...GTP....DM..R
RetrocopyCET*ALILALTRELAVQIKKGLLTLGNYVNVQCHACIGGTNVGEDIQKLDYR-QHVVAGTPR--YDMIRR
ParentalRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRIL-VK
R.L....IKM...DEADEML..GF...IY.....L...T.VVL.SA..P...LE.TKKFM.DPI.I..V.
RetrocopyRSLRTRAIKMLIWDEADEMLNKGFIELIYNVHLYLPPAT*VVLISAMLPHKILEMTKKFMTDPIHIR<VM
ParentalKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMD
..EL.LEGI.QF....E.EEWK.D..CDLY.TLTITQA.IF.NT.RKVDWL.EK.....FTV..MH.DM.
RetrocopyRDELILEGIKQFFVVLE*EEWKFDRPCDLYDTLTITQAIIFCNTKRKVDWLPEKICKANFTVLCMHRDMP
ParentalQKERDVIMREFRSGS-SRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRF-GRKGVAINM
QKE...IM.EFRSG..S.VLI.T...ARG.DV.QVSL...YDLP.NR..Y.HRIG..GR...RKG.AIN.
RetrocopyQKECQSIMKEFRSGA<SSVLISTHVWARGLDVPQVSLIVTYDLPNNR*LYTHRIGKSGRY>SRKGMAINF
ParentalVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
V...D....RDI...Y.T.I.EMP.NV..LI
RetrocopyV*NNDICIHRDIKQYYSTQIDEMPMNVVYLI

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Sorex araneus was not studied using ChIP-Seq data.

EST - click to see more details

Sorex araneus was not studied using EST data.

TSS - click to see more details

Sorex araneus was not studied using FANTOM5 data.

Lab - click to see more details

retro_sara_605 was not experimentally validated.

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 21 parental genes, and 81 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000167531 retrocopy
retro_amel_1300,
Callithrix jacchus ENSCJAG000000151148 retrocopies
retro_cjac_1876, retro_cjac_2046, retro_cjac_2521, retro_cjac_2679, retro_cjac_3086, retro_cjac_3203, retro_cjac_395, retro_cjac_727,
Cavia porcellus ENSCPOG000000049001 retrocopy
retro_cpor_1088,
Dipodomys ordii ENSDORG000000142251 retrocopy
retro_dord_732,
Erinaceus europaeus ENSEEUG000000035811 retrocopy
retro_eeur_610,
Felis catus ENSFCAG000000248971 retrocopy
retro_fcat_370,
Homo sapiens ENSG0000016196010 retrocopies
retro_hsap_1004, retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836, retro_hsap_4873, retro_hsap_4931, retro_hsap_610,
Gorilla gorilla ENSGGOG000000247028 retrocopies
retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
Macropus eugenii ENSMEUG000000107802 retrocopies
retro_meug_158, retro_meug_179,
Microcebus murinus ENSMICG000000147592 retrocopies
retro_mmur_1164, retro_mmur_1477,
Myotis lucifugus ENSMLUG000000034153 retrocopies
retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta ENSMMUG000000134991 retrocopy
retro_mmul_1280,
Monodelphis domestica ENSMODG000000070903 retrocopies
retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Mus musculus ENSMUSG000000597967 retrocopies
retro_mmus_1810, retro_mmus_1853, retro_mmus_2320, retro_mmus_2473, retro_mmus_3122, retro_mmus_325, retro_mmus_527,
Nomascus leucogenys ENSNLEG000000095477 retrocopies
retro_nleu_2109, retro_nleu_2117, retro_nleu_230, retro_nleu_2470, retro_nleu_2769, retro_nleu_440, retro_nleu_701,
Otolemur garnettii ENSOGAG000000081322 retrocopies
retro_ogar_1375, retro_ogar_1862,
Ochotona princeps ENSOPRG000000085912 retrocopies
retro_opri_155, retro_opri_985,
Pan troglodytes ENSPTRG0000000869410 retrocopies
retro_ptro_1201, retro_ptro_1465, retro_ptro_2954, retro_ptro_3112, retro_ptro_3247, retro_ptro_450, retro_ptro_750, retro_ptro_810, retro_ptro_862, retro_ptro_870,
Rattus norvegicus ENSRNOG000000306283 retrocopies
retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Sorex araneus ENSSARG00000006017 7 retrocopies
retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605 , retro_sara_89,
Ictidomys tridecemlineatus ENSSTOG000000248141 retrocopy
retro_itri_610,


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