RetrogeneDB ID:

retro_sita_4

Retrocopy
location
Organism:Foxtail millet (Setaria italica)
Coordinates:5:31269708..31272594(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:Si005170m.g
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Si000029m.g
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sita_4
ATGAGGAATCAGCTGAAAGATACAATGGACAAATGCAACCTCCTATCATCAGAAGTTGAGAAGGCCCAACAGGCTGAGAA
AGAAGTGCATGCCTTGTTGGAAGAAAACCAGAAGCTGAAGAATGATAACTTGATGCTGTTGGTTGAGCATGATAACCTGA
AAGCACTTCATCAGAATTTAGATGTTGAGTGCTTTCAACTGAAGGCAGCCATTGCAGAAATCACCGCTGAAAATGAATCC
TTGATCACAGAAAATCATTCAGCTGAAAGAAAACTCCAGCAACTGGGGTTGGAGATAGATGGCCTGAAAGTCGAGGCCGC
AGAGTTAATGAACAATCTAGACAAGGAGCGTAATAATGCAGCAGAAGAAAAAGAAAGACTAGTATCAGAAAATTCCATAT
ACTTGAATGAGATAGAGAAGGCACAGTCTAGTATTAAAGATCTAGAAAAGGAACTGGAATCAACAAGAAATGTTATGAAT
AGTAATATGGCCGAGCTACAGGAGGAGAAGGATTCGGCCATGTCAGAGGTAGAGCAGCTAGAGGCTTCTTTGATGAATCT
TAAGACTGAGCTAGCACAACAACTTGAGAGGATTTCAGATATGCAGAAGACTACTGAAGAACTGGAGCTGGCAAATTCTA
ACATGCATAATGAAATTGTAGAAGTAAAAGGACAAAAAAATGAAGCTGCTGCTTCTGTTATTAATCTTGAAAGCAATTTA
GAACAACAAGTTGAACAAATTTCTGTTCTGCAGCTTTCTAATGAAGACCTACAAAATAGTAACTCCAACCTGAAGATGCA
ACTGGAAGAGGCGAAGGTTAGTCACCATGCTGAAATTTTAGCATTACAAGATGAAAGGAACAAAATAATTTCAGATCTGC
AGCAGTCTGAGGCTTCTATCAAGAATCTTAGAATTGAATTGGAGCAAGGAAAAGAGCAAATCTCAAAAATGAATCTAGCT
AATGAAGATCTGAAGAACAACATTGCTATATTGGACAAGCAATTGGAGGAGGTCAGGAGCAGTTTGCATGCTGAAATTGC
ACAACTACAAGCAGAGAAGGGCATAGTTCTATCAGAGTTACAGGTGTCTCAGGCTTCTGTCAGAAACTTGGAGAGTGTGC
TAAAAAAGCAAAGTGAGAAGATTTCAACTCTGGATCAAGCTAATGATCAGTTACAGAAAAACATATGTACCTTGACTGAG
CAATCAGAACAAACCAAGGCTGAGCTGCAGAAGGAGGTTGAGGCAACACAAGAAGAGAAGGATACAACACTAACACAACT
AAAGCAGTCACAGACTTCAGTACAAAATCTTGAGAATGAGGTGACACGACTGAAAGAGGATCTTTCAGTTCAGCTAGAAA
GCAATTCCACCTTGGACAAGCAGTTGGAAGAAGTCAGGAGCAGTACGCATGCTGAAATTGCAGAACTACGTGCAGAGAAG
GACGCAACGCTATTGGAGTTACAGACGTCTCAGGCTTCTGTCAGAAATCTTGAGATTGCCCTTCAAACCCAAAACGAGAA
CATTTCAACTCTACAGCAAGCTAATGATGAGTCACAGAAGATCATTTGTACTTTGACCGAGCAATCAGAACAAGCCAAGG
CTGAGCTGCAGCAGGAGGTTAAGGCTACACAAGAAGAGAAGGATGCAGTGCTAACAAAGCTGAAGCAATCAGAGGATTCA
GTACAAAATCTTGCGAATGAGGTGACACAGCTGAAAGATGAACTTTCAGTTCAGCTGGAAAATAATTCTACCTTGGAAAA
GCAGTTGGAAGAGGCAATACTAAAAGTATCTAACCTACATGAGAATCTCGAGAAGGCTCAGGCTGAAGCAGCTTGTCAAA
TTGATGACATGAGTACAAAAACAAAAGATCTGGAGAAGACAATCGCTCTATTGTCTTATCAAAAGACCAAGTTGGAGGAG
GATCTAAAAATTATGATTGAAGCATGCACAGTAAACATGTCATTTATGACGGAATTTGAAGATAGAGTTACACAAAAAAA
TTCAGATCATGAGGCTGGACTTGTGGTTCTCCGCCAGAGCCTGAAAGGGGTTGCTAGCAGCTGTCAGAGGCTTCAGTATG
CATATGATGAGGTGTCCTCGAGGGTCTCCCAGCTCGAGATACTTAAGAGGCTTCAGATTGAGCAGATAGGTCAACTAGAG
GAGAAACACACAGAAACTTTGGAGAAACATCGACTTCTGGAAGAGGAAAATTTATCTGCAAATAAGGAGAACACAAAGCT
ACAAAAGGATGTCCAAGACCTTGAAGTTCAACTCCAGCTAGCCAAGCAGAAGCTTAAAGTTACCGAGGCAGAAAGCAAAT
GCAAAGAAGACAGCTACGCAATGGCAGTGGAGACATCACAGGCAGAGATCCATCATCTTGAACAACTGGTAAAACAATTT
TCTGGGAGAGTCAACTTGCTGGAAGAAACTCTCATGCAAGTAAAAGGACATGCCGAATCAGGGGTCTCTGAATTGGCTGA
CAAATTGGACGAGCTAGAACCACTCTTGTGTCAGAGTTTTGCACTCTTCGTTGATCGTTCATCTGCATGTGGTGAAGAGC
TTAATGTCCTGAGGAAGAAGCTACATGATCATCTTGATGAACAGAAGGAGCTTGTCAAGGAGAATGATGAGATGGCTGTC
AGGTTGAGAGAGAAAGAAAAATTGGTGTCAGAAATGGTGAAGAACACAGCTGATGCAGAAGCGAAGATGGTCCAGCTCGA
GAAGACGGTGGCAGAGAAAGAAGAAGAGCTAGCAGCTAGAGTGCAGGAGAAGAGAGAAGCCATTAAGCAGCTGAGCGACG
CGATTGTTTACCACAAGAACTATAGCGATGATCTGGTGCGCTACATCCGCAGTCACAATCGCCCTCGCCTCCCATTCTGT
CTGTAA

ORF - retro_sita_4 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.21 %
Parental protein coverage: 50.88 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalNLHNEIVELHGQKNEAADSVINLESKLEQQ----VQEISNLQKANKDLKAAKTDLYNEITALQEEKNAAL
NL....VE...Q.............KL.........E..NL......L......L...I.....E.....
RetrocopyNLLSSEVEKAQQAEKEVHALLEENQKLKNDNLMLLVEHDNLKALHQNLDVECFQLKAAIAEITAENESLI
ParentalAQLQESEANIKKLQSDLRVEQISDLQLANEDLQKSNSKLKMQLEEAKFSHQAEILALQDEKNKIISDLQQ
......E.....L.............L.N..L.K.........E...................I......
RetrocopyTENHSAERKLQQLGLEIDGLKVEAAELMN-NLDKERNNAAEEKERLVSENSIYLNEIEKAQSSIKDLEKE
ParentalSEASIKILVSNIAELQKDNDSAMSEIEQLEASLMNLKTELAQQLERISDMQKTNEGLELANSNLHNEIVE
.E.......SN.AELQ...DSAMSE.EQLEASLMNLKTELAQQLERISDMQKT.E.LELANSN.HNEIVE
RetrocopyLESTRNVMNSNMAELQEEKDSAMSEVEQLEASLMNLKTELAQQLERISDMQKTTEELELANSNMHNEIVE
ParentalLQGQKNEPATSVINLESKLEQQVQEISKLQEANKDLEAGKTDLYNEVMALQAEKNAALAQLQQSEANIKE
..GQKNE.A.SVINLES.LEQQV..IS.LQ..N.DL......L............A....LQ........
RetrocopyVKGQKNEAAASVINLESNLEQQVEQISVLQLSNEDLQNSNSNLKMQLEEAKVSHHAEILALQDER---NK
ParentalLQSDMVQQQNQILHFQRENEEMQSTNSRLHKQLEEIRTNLQDEIIVLQGEKEEAINSLHQSNDSVKTLR-
..SD..Q....I.....E.E......S......E....N....I..L....EE...SLH...........
RetrocopyIISDLQQSEASIKNLRIELEQGKEQISKMNLANEDLKNN----IAILDKQLEEVRSSLHAEIAQLQAEKG
Parental-VQLEQQVEQISVLQLANEDLQNINSRLKMQLEEAKCSHQAEILALQDE----KNKIISDLQQSEASIKN
.V..E.QV.Q.SV..L..E......S.....L..A....Q..I..L.......K................
RetrocopyIVLSELQVSQASVRNL--ESVLKKQSEKISTLDQANDQLQKNICTLTEQSEQTKAELQKEVEATQEEKDT
ParentalLRIELKQGKEQI----SEMNLSNEDLTNNI---AILNKQLEEVRSSLHAEIAQLQAEKGIVLSELQVSQA
....LKQ..........E.....EDL.........L.KQLEEVRSS.HAEIA.L.AEK...L.ELQ.SQA
RetrocopyTLTQLKQSQTSVQNLENEVTRLKEDLSVQLESNSTLDKQLEEVRSSTHAEIAELRAEKDATLLELQTSQA
ParentalSVRNLESVLEKQSEKISTLDQANDQLQKNICTLTEQSEQTKAELQKEVEATQEEKDTALTQLKQSQTSVQ
SVRNLE..L..Q.E.ISTL.QAND..QK.ICTLTEQSEQ.KAELQ.EV.ATQEEKD..LT.LKQS..SVQ
RetrocopySVRNLEIALQTQNENISTLQQANDESQKIICTLTEQSEQAKAELQQEVKATQEEKDAVLTKLKQSEDSVQ
ParentalNLENEVTQLKDELSVQLENNSTLEKQLEEAILKVSNLHENLEKAQAEAACQIDDMSTKTKDLEKTIDLLS
NL.NEVTQLKDELSVQLENNSTLEKQLEEAILKVSNLHENLEKAQAEAACQIDDMSTKTKDLEKTI.LLS
RetrocopyNLANEVTQLKDELSVQLENNSTLEKQLEEAILKVSNLHENLEKAQAEAACQIDDMSTKTKDLEKTIALLS
ParentalCRKTKLEEDLKIMIKACIVNMSFMTEFEDRVTQKISDYEAGLVALHQSLKGVTSSCQRLQYAYDEVSSRV
..KTKLEEDLKIMI.AC.VNMSFMTEFEDRVTQK.SD.EAGLV.L.QSLKGV.SSCQRLQYAYDEVSSRV
RetrocopyYQKTKLEEDLKIMIEACTVNMSFMTEFEDRVTQKNSDHEAGLVVLRQSLKGVASSCQRLQYAYDEVSSRV
ParentalSQLEILKRSQIEEIGQLEVKHTETLEKHRLLEEENLSANKVNTKLQKHVQDLEVQLQLAKQKLKVTEAES
SQLEILKR.QIE.IGQLE.KHTETLEKHRLLEEENLSANK.NTKLQK.VQDLEVQLQLAKQKLKVTEAES
RetrocopySQLEILKRLQIEQIGQLEEKHTETLEKHRLLEEENLSANKENTKLQKDVQDLEVQLQLAKQKLKVTEAES
ParentalKCKEDSYAMAVETSQAEIHRLEQLVKQFSGRVSLLEETLMQVKGHAVSGVKVLRKKLHD
KCKEDSYAMAVETSQAEIH.LEQLVKQFSGRV.LLEETLMQVKGHA.SGV..L..KL..
RetrocopyKCKEDSYAMAVETSQAEIHHLEQLVKQFSGRVNLLEETLMQVKGHAESGVSELADKLDE

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






RNA-Seq - click to see more details

Setaria italica was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Setaria italica was not studied using ChIP-Seq data.

EST - click to see more details

Setaria italica was not studied using EST data.

TSS - click to see more details

Setaria italica was not studied using FANTOM5 data.

Lab - click to see more details

retro_sita_4 was not experimentally validated.

Retrocopy orthology:
Setaria italica 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Setaria italica Si000029m.g 1 retrocopy
retro_sita_4 ,




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