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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACAGAATTATTCATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatatttgcaacagctattgaccttacaatttaactacagtttaaatgaacctataaactgtgacattcagaaatatttcttgctgcttgaaacaag...

Basic information

species Zea mays
transcript GRMZM2G094978_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094978_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 3
AAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACAGAATTATTCATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtca-atatttgcaacagctattgacctta-caatttaactacagtttaaatgaacctataaactgtgacattcagaaatatttcttgctgcttgaaacaag---
||||||||||||| || ||||| || ||||||||||||||||||||||||||||| || |||||||| ||||||||||| |||||||||||||||||||||||| ||||||   |    | | ||| ||| ||| |||| | || || ||| |  |  | |  ||  || || | |   |  | |||  |  |  ||   ||   
AAAGAAAGGAGTTTATTGCTTCGCTGCACAAGAGGAAAACAGAATTATTCATGGCTCTGATTGAGAAGAAGTTGCTTCCCCTCCGTCCAGGTGTTCAAAGgtcatatattttacatgaatttggactttagcaacttaa-tgcacttcaaaagttctaaca--cttcgatatcctgctttgctactt--taatacaagtcagtta

upper sequence: GRMZM2G094978_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G18320.1 (Glycine max), 5'ss of exon 4
AAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACAGAATTATTCATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTT-CAAAG-
||||||| || ||||||||||| || |||||    || |||||| |||| |||||||| |||||||||||  || | ||||| |||||||||||| |||||   || | ||| ||  |   | || ||  ||      |||| ||| | |    ||   |   | ||| |   ||  |     | ||||| |||| |  |           
AAAGAAAAGAATTCATAGCTTCACTCCACAAACAAAAGACAGAACTATTTATGGCCCTTATTGAGAAAAAACTGTTGCCTCTTCGTCCAGGTGTTGCAAAgttggttactatctgttctttatcttttatccaatttgtttatctataatggtttttgttaggcgtatgatgatgataagagaaaaaatagttctagggg-----------

upper sequence: GRMZM2G094978_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 3
AAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACAGAATTATTCATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatatttgcaacagctattgaccttacaatttaactacagtttaaatgaacctataaactgtgacattcagaaatatttcttgctgcttgaaacaag-
|||| ||||| ||||| ||||||||||||||| | ||||| ||||| ||||||| ||| |||||||||||  |||| ||||| || || ||||||  || |||| | | ||    | ||  ||   | |     ||  |    ||   || |   |  | |   |       |  | |    |||||  |||         
AAAGGAAGGAATTCATTGCTTCTCTTCACAAGCGAAAAACTGAATTGTTCATGGTCCTGATTGAGAAAAAACTGCTGCCTCTTCGACCCGGTGTTGCAAAgtcagt-tctgtttgatcttctgctttaatgtgctatattttattgttattattattaacatgattgttgcaattagtccaccttgcatcttttggtcgta

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|211136606|gb|FL156037.1|FL156037
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|91056651|gb|EB167069.1|EB167069
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|149014075|gb|EE043602.2|EE043602
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|86467368|gb|DY233738.1|DY233738
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|149112364|gb|EE295251.2|EE295251
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|211136608|gb|FL156039.1|FL156039
EST:     TGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCCGTCCAG-TGTTCAAAA                         GTTAATCGATGAAGCTTTAGGAAA
genomic: TGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCC-GTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAA
EST: gi|50333792|gb|CO528918.1|CO528918
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|71764323|gb|DR962260.1|DR962260
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|71300514|gb|DR786312.1|DR786312
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|101382873|gb|EB813490.1|EB813490
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|71448345|gb|DR829395.1|DR829395
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|86467369|gb|DY233739.1|DY233739
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|71300530|gb|DR786320.1|DR786320
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|50327117|gb|CO522243.1|CO522243
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|101388003|gb|EB816016.1|EB816016
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|71766392|gb|DR964329.1|DR964329
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 67

AAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACAGAATTATTCATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 417

AAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACAGAATTATTCATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 16

AAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACAGAATTATTCATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 85

AAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACAGAATTATTCATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT