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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcatagatttgggctaagcatactttttacggtataatctcactaactgtgctgattaagttctgttgctgtttctttgttacaaaag

Basic information

species Zea mays
transcript GRMZM2G014136_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014136_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 5'ss of exon 2
TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcatagatttgggctaagcatactttttacggtataatctcactaactgtgctgattaagttctgttgctgtttctttgttacaaaag---
||||||||||||||||||||||||||| ||||||   | ||| |||||||||| |||||||||||||||| | ||||||||||| || ||||| ||||||||| |||   | |||| ||  ||      ||  |    | || | |   || ||||| |||| |  || |  |     || ||||    |   |   
TCTTGGAACAAAGCGCCACCATGACAAATGGTTGTCGGACACAGAAAATTATGTTATCAAGGGTTGTTTTTCCATGACAGAACTGGGTCATGGGAGCAATgtatgtgatgatattttggtcaaa-----ttactgaattgtagttttgttagctgtgttgatgagatttttctttgccttatttgactaatttgaag

upper sequence: GRMZM2G014136_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA06G43840.1 (Glycine max), 5'ss of exon 2
TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcatagatttgggctaagcatactttttacggtataatctcactaactgtgctgattaagttctgttgctgtttctttgttacaaaag-----------
||| ||||| |||||||| |||||||||||||||  | | || ||||| ||||||||||||||||||||||| ||| | ||  ||||||||||||| |||||| ||| |      |     |       |  |||       || | | | | | ||||  |    |     |  |  |  |   || || |             
TCTGGGAACCAAGCGCCATCATGACAAGTGGTTGAATTCTACTGAAAACTATGATATCAAGGGTTGTTTTGCTATGTCTGAGTTAGGCCATGGAAGTAATgtatgtgaaggttgctcaataagttggggtcattagttccacatgtaaattattatgcttttgccttgtcacttttaataatcccttccagactaattttcatag

upper sequence: GRMZM2G014136_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA12G14060.1 (Glycine max), 5'ss of exon 2
TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcatagatttgggctaagcatactttttacggtataatctcactaactgtgctgattaagttctgttgctgtttctttgttacaaaag-----------
||| ||||| |||||||| |||||||||||||||  | | || ||||| ||||||||||||||||||||||| ||| | ||  ||||||||||||| |||||| ||| |  | |      ||||     |  ||| |     || | | | | | ||||  |    |     |  |  |  |   || || |             
TCTGGGAACCAAGCGCCATCATGACAAGTGGTTGAATTCTACTGAAAACTATGATATCAAGGGTTGTTTTGCTATGTCGGAGTTAGGCCATGGAAGTAATgtatgtgaa-ggttgcccaataagttgggtcattaggtctacatgtaaattattatgcttttgccttgtcacttttaataatcctttccagactaattttcatag

upper sequence: GRMZM2G014136_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G06290.1 (Arabidopsis thaliana), 5'ss of exon 2
TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcatagatttgg--gctaagcatactttt--tacggtataatctcactaactgtgctgattaagttctgttgctgtttctttgttacaaaag
| ||||||||||||| |||||||| |||||| ||     ||| ||| |||||| | ||||||| |||||||| ||||| || |||||||||||||| |||||| |   ||    |||   || |    |  | |   || |  ||  |     |     |    ||| |||||| ||  | ||  |||| || |    
TTTTGGAACAAAGCGTCACCATGAAAAGTGGCTGAAGAACACCGAAGATTATGTTGTCAAGGGCTGTTTTGCTATGACTGAGCTAGGCCATGGAAGTAATgtaggcatattttcttgattgccattttttttctccatatgtcatggtgatcttccacatttatattgagttctatttat-ttcttttgatatag---

upper sequence: GRMZM2G014136_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G06310.1 (Arabidopsis thaliana), 5'ss of exon 2
TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcatagatttgggctaagcatactttttacggtataatctcactaactgtgctgattaagttctgttgctgtttctttgttacaaaag
  |||| |||||||| |||||||| |||||| ||   | ||| ||| |||||| | ||||||| || ||||||||||| || |||||||||||||  |||||| |   || |     |  | |   | | |||  |   |  || |   ||   ||| |  || | ||  || ||| |                
CTTTGGGACAAAGCGTCACCATGAAAAGTGGCTGAAAGACACTGAAGATTATGTTGTCAAGGGCTGCTTTGCAATGACTGAGCTAGGCCATGGAACTAATgtaggcatattg---cagtgtcattttgcatttatccagactatatatgtattggtgatctttga-tttggtggctttcag-------------

upper sequence: GRMZM2G014136_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv12s0028g02660.t01 (Vitis vinifera), 5'ss of exon 2
TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcatag---------atttgggctaagcatact----ttttacggt-ataatct-cactaactgtgctgattaagttctgttgctgtttctttgttacaaaag
| ||||||| ||||| || |||||||||||||||   | ||  || |||||||  ||||| ||||| ||||||||||||||| | || |||||||| |||||| ||| |            ||||||  |  |   ||      | || | | ||  ||| || |  |  || || |||  ||   ||| |  ||   ||   ||    
TTTTGGAACCAAGCGTCATCATGACAAGTGGTTGAGAGACAGTGAGAATTATGTGATCAAAGGTTGCTTTGCAATGACAGAATTGGGGCATGGAAGTAATgtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcag---

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|211531376|gb|FL093845.1|FL093845
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211534374|gb|FL093854.1|FL093854
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211306090|gb|FK992685.1|FK992685
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAAAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|50322995|gb|CO518121.1|CO518121
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211534377|gb|FL093857.1|FL093857
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|78118417|gb|DV536803.1|DV536803
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211531379|gb|FL093848.1|FL093848
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211534383|gb|FL093863.1|FL093863
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211534378|gb|FL093858.1|FL093858
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|78122592|gb|DV540976.1|DV540976
EST:     ATGATATCAGGGGTTGTTTTGCAATGACAAAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAAAAACAATAGCAACTTATGATTCAAAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211531380|gb|FL093849.1|FL093849
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211531373|gb|FL093842.1|FL093842
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211531377|gb|FL093846.1|FL093846
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211531369|gb|FL093838.1|FL093838
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211537384|gb|FL093868.1|FL093868
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211534380|gb|FL093860.1|FL093860
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211537385|gb|FL093869.1|FL093869
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211534371|gb|FL093851.1|FL093851
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211531381|gb|FL093850.1|FL093850
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|74241999|gb|DT649913.1|DT649913
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
EST: gi|211534385|gb|FL093865.1|FL093865
EST:     ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAAT                         GTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC
genomic: ATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTC

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: 101

TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTCATCATAAATACTCCATGTGAATCAGCTCAGAAGTACTGGATTGGTGGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 368

TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTCATCATAAATACTCCATGTGAATCAGCTCAGAAGTACTGGATTGGTGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 534

TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTCATCATAAATACTCCATGTGAATCAGCTCAGAAGTACTGGATTGGTGGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 115

TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcat ... gttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTCATCATAAATACTCCATGTGAATCAGCTCAGAAGTACTGGATTGGTGGAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAACTAGGCCATGGAAGCAATgtacgtgcatagatttgggctaagcatactttttacggtataatctcactaactgtgctgattaagttctgttgctgtttctttgttacaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA