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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctatgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcag

Basic information

species Zea mays
transcript GRMZM2G104373_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 4
TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctatgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcag
 |||||||||||||| ||||| |||||||| || ||||| || ||||||||||||||||| || ||||| ||| | || || ||| |||| ||||||||||||||| | |   |||     ||   ||| ||||  | ||       || | || || ||| ||| ||| |    |||||   | ||||
CATTGAAAGTCTTGACCCAGCTTTGCTTCGACCTGGTCGGATAGACAGAAAGATTGAATTTCCGTTACCAGATATTAAAACCAGGAGGCGGATCTTCCAGgtgcttttctacaatg-----tttcaagttctgtcttattgg-----aaacctgcttcgttcttatcaata----gtttttgggtgcag

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G27200.1 (Glycine max), 5'ss of exon 4
-TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctatgtgatgaaagcttctgagt-cctgttcttttaattaaaaagcatgatttgttgttaccaaaattt--tgttttgatgagcag
  |||||||| ||||||||| || || | || || |||||||||||||| |||||||||||    |||  |  ||  || | |  || |    | |||||       || ||||    |  |   | ||| ||||   |  | ||| | |       ||| ||| ||   | |||   || ||| ||  | ||
GAATTGAAAGCCTTGATCCAACCCTGTTGCGACCTGGTCGAATTGACAGGAAGATTGAATTGGTATTAAGTT-TGCAAAAAGT--GCAGTTACTATTCCAA------CTgtgtggaatattcaagtcagtacctggcttcgttattgagag------tttcttgctaatgagattgaatgcttttatt-gtag

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctatgtgatgaaagc---ttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcag---------------------
 |||||||| ||||||||||| ||||| || || |||||||||||||| ||||||||||| ||| | |||||| | || || ||  | ||||| ||||||||      || |  |||||||   || | |||     |  || | |   | | | | || || |  | | |     || | |   | |   |                     
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacattttgtgaaagcaagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttag

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 4
TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttct-----atgtgatgaaagcttctgagtcctgttcttttaa---ttaaaaagcatgatt------tgttgttaccaaaattttgttttgatgagcag
 |||||||||||||||||||| ||||| || || |||||||||||||| ||||| ||||| ||| | |||||| |||| || ||| | ||||||||||||||     |     || |  |||||||     |  | |||  ||   |    |  |  || || |       |||| || |   | |||||||||  |      
AATTGAAAGTCTTGATCCAGCTTTGCTACGACCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTCCAGgtaggcatgactaattttgtgaaagcaatacacccatgtgtttgggaaagcttgatggcctggtccatttgtgttctttctttagttttgtttttgtttt---

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G04920.1 (Glycine max), 5'ss of exon 4
TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgc----------ttctatgtgatgaaagcttctgagtcctgttcttttaat-taaaaagcatgatttgttgttaccaaaattttgttttgatgagcag
 |||||||||||||||||||| ||||| || || |||||||||||||| ||||| ||||| ||| | |||||| |||| || ||| | |||||||| |||||            || | ||  |  ||  |  ||      ||||     ||| |  |  || || |   ||  |        ||| ||||  |      
AATTGAAAGTCTTGATCCAGCTTTGCTACGGCCTGGTCGAATTGACAGGAAGATAGAATTTCCTCTTCCTGATATCAAAACAAGGAGACGCATCTTTCAGgtaggcatgactaattttgtgaaagcaatacacctaccatgtgtttgggaaatcttgatggcctggtccatttgtgttctttctttatttttgttttttt

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G35510.1 (Glycine max), 5'ss of exon 4
TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctatgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaa-------aattttgttttgatgagcag---------------------
 |||||||| |||||||||||| |||| || || |||||||||||||| ||||||||||| ||| | |||||| |||| || ||  | ||||| |||||||    ||    |||  |   ||    |  | |||| ||    || |    |||   ||  | || | |        | || | | |   | |   |                     
AATTGAAAGCCTTGATCCAGCCCTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATCAAAACAAGAAGACGCATTTTCCAGg----tcggaatgactagttctgtgaaaacatgtttttggttttcactgacatatcttaatattcctattctacttagttatatctcactaaaaggtcttatacttttgatatttag

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctatgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaa---------aattttgttttgatgagcag--------------------------------
 ||||||||| | |||||||| |||||||| || |||||||| || || ||||||||||||||| | |||||  | || || ||  | ||||| |||||||| | | | |||  | | |   |   | | |  |  |    ||          || || |||| || |          ||   ||  ||||| |  |                                 
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtt-taagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag

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|149110574|gb|EE294195.2|EE294195
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGGGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|37401158|gb|CF637942.1|CF637942
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|60394503|gb|DN227373.1|DN227373
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|87156235|gb|DY401024.1|DY401024
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|71318153|gb|DR795840.1|DR795840
EST:     AGATTGAATTCCCTTTTCCTGATGTCAAGACTAGGCGGCGCATTTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|40302995|gb|CK347382.1|CK347382
EST:     CAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: CAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|60399673|gb|DN232483.1|DN232483
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|6828042|gb|AW331685.1|AW331685
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|74232019|gb|DT639933.1|DT639933
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|5895801|gb|AW037047.1|AW037047
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|4887302|gb|AI677401.1|AI677401
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|47961685|gb|CN844394.1|CN844394
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|21987487|gb|BQ779015.1|BQ779015
EST:     AGATTGAATTCCCTTTCCCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACAGTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|60357188|gb|DN224161.1|DN224161
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|20301592|gb|BQ164535.1|BQ164535
EST:     AGATTGAATTCCCTTAACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|74232018|gb|DT639932.1|DT639932
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGGGCATTTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|78103532|gb|DV521960.1|DV521960
EST:     TGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: TGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|211268017|gb|FL355150.1|FL355150
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|76917636|gb|DV166930.1|DV166930
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|78023275|gb|DV491662.1|DV491662
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|5650117|gb|AI920477.1|AI920477
EST:     CGGCGCTTCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: CGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|32847761|gb|CD987442.1|CD987442
EST:     AGATTGAATTCCCTTTACCCGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|78544201|gb|DV621699.1|DV621699
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|67015613|gb|CO444362.1|CO444362
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
EST: gi|6022662|gb|AW067474.1|AW067474
EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

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: 48 (upstream exon), 48 (downstream exon)
Score: 215

TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 359

TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 431

TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 328

TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA