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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttagattggattcaaatgtattgcttgagtcataaaatcttttggatcaacttaatttagcaccgtacaacttagatttcttgttgcctttcttc...

Basic information

species Zea mays
transcript GRMZM2G035338_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035338_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g40880.1 (Oryza sativa), 5'ss of exon 8
GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttag-attg--gattca-aatgtattgctt----gagtcataaaatcttttggatcaacttaatttagcaccgtacaacttagatttcttgt-tgcctttcttc
|||||||||||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||||| |||| |||||  ||||  ||| || ||| ||||   |       |   | |||  ||    || | ||   |||   |  |  || | | || |   |  |||        
GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCAgtgagttatcattgcagatccagaatatattctctttgtagattgcagaatgcttgaactctagttt-cttatttcgatttaaatcaaatgtgaagcatgc--------

upper sequence: GRMZM2G035338_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G34390.1 (Glycine max), 5'ss of exon 8
GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttagattggattcaa-atgtattgcttgagtcataaaatcttttggatc-aacttaatttagcac-cgtac-aacttagatttcttgttgcctttcttc
|| ||||||||||  ||||||||||| ||||||||||| |||||||||||  |||| || ||||| || |  |||| |||    |   ||| || ||||  | |     |||  |  |  ||    ||  ||  || |||  |    ||   |   | | |   || ||   |     
GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatcttaacatttaagatgtggtccactcatcagcattttattaatttctgacacaaattatgatatatattgaacaaaagtaaatgatgaaata----

upper sequence: GRMZM2G035338_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT1G03030.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttag-attggattc--aaatgtattg--cttgagtcataaaatcttttggatcaacttaatttagca---ccgtaca-acttagatttcttgttgcctttcttc--
|| ||||||||||  ||||||||||||||||| ||||| || ||||||||  |||| || ||||| |  |  ||||||||    | | | |||  |||| | |       || || ||   |  | || |     ||  |||  |    ||| | | | | || |  ||| |  ||| |  |   
GGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCAgtaagtagtcagtagcttcctaaatctgtcaaatccgaatc-tagtgtaatatgaaatggttttgtttgcctattccggagacagtcagctaacttatgtcctcttcttag

upper sequence: GRMZM2G035338_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv07s0141g00310.t01 (Vitis vinifera), 5'ss of exon 8
GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttagattggattcaaatgtattgcttgagtcataaaatcttttggatcaacttaatttagcaccgtacaacttagatttcttgttgcctttcttc---
|| ||||||||||| ||||| ||||||||||||||||| || ||||||||  |||| |||||| | |  |  ||||||||   |||   |||      || | |    | || ||    |   |    | || ||   | || |      |  ||    || |    |   |     
GGGTCAGTTTATGCACCATCGTTTGATCATGGTGTTGGAGATCCAGTTGAAGATGATATATTTATCAGCCTCCAgtaagt--aatttacttctttcacatagataatcttatcaacagctgccg-ctgatttcataatgaactgggtgtttatgaacatttatccagtccatatgat

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|89106837|gb|DY577054.1|DY577054
EST:     GATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA                         GCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
genomic: GATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
EST: gi|26558613|gb|CA830848.1|CA830848
EST:     GATCATGG-GTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA                         GCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
genomic: GATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
EST: gi|89106843|gb|DY577060.1|DY577060
EST:     GATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA                         GCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
genomic: GATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
EST: gi|166510545|gb|EG255544.1|EG255544
EST:     GATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA                         GCACAAAATAGTGATAGTTGAAGGGAACTA
genomic: GATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTA
EST: gi|26558572|gb|CA830807.1|CA830807
EST:     GATCATGG-GTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA                         GCACAAAATAG-GATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
genomic: GATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
EST: gi|22545958|gb|BU098317.1|BU098317
EST:     GATCATGG-GTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA                         GCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
genomic: GATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
EST: gi|22472530|gb|BU037010.1|BU037010
EST:     GAGAATGACATATTTGTAAAGCCACA                         GCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT
genomic: GAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 85

GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87

GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 95

GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 70

GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttaga ... actttggcagGCACAAAATAGTGATAGTTGAAGGGAACTATCTGTTACTGGAAGAAGATGTTTGGACCGAAATTAGAGACTTGTTTGATGAGAAATG