Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgcctgctgattctgagcctttattatctgcactgatcttcccctgatttcaccagttttacaatcatgtctcattctcatgatgtgcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGCATGGTGTTGTTCCGAGGCATGCCGCTCAATTGGTAGAGAGCAGAAGCCT

Basic information

species Zea mays
transcript GRMZM2G060511_T02
intron # 1
splice site 3'
intron type U2

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|211105374|gb|FK962294.1|FK962294
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|6918506|gb|AW400036.1|AW400036
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|16925121|gb|BM078189.1|BM078189
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|211120812|gb|FL379842.1|FL379842
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|76013587|gb|DT940757.1|DT940757
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|78108428|gb|DV526846.1|DV526846
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|211406014|gb|FL414971.1|FL414971
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCGGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAGGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|211489492|gb|FL457175.1|FL457175
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCATGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|60356072|gb|DN223045.1|DN223045
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|211482104|gb|FL397163.1|FL397163
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|71310490|gb|DR791540.1|DR791540
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTGGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|71310492|gb|DR791541.1|DR791541
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|71773314|gb|DR971222.1|DR971222
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|211539867|gb|FL420835.1|FL420835
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|211127647|gb|FL428283.1|FL428283
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAGGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|78107093|gb|DV525511.1|DV525511
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|78107094|gb|DV525512.1|DV525512
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|211118506|gb|FL407768.1|FL407768
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|76917703|gb|DV166965.1|DV166965
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|148980404|gb|EE027114.2|EE027114
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|78179190|gb|DV549563.1|DV549563
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|71773313|gb|DR971221.1|DR971221
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|76013586|gb|DT940756.1|DT940756
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|50335756|gb|CO530882.1|CO530882
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|12046406|gb|BF728545.1|BF728545
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
EST: gi|211309358|gb|FL406192.1|FL406192
EST:     CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAG                         TGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC
genomic: CCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGC

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: 49 (upstream exon), 49 (downstream exon)
Score: 99

TCCCTCGAGGCCTTCCTCCCCACCGGTTCAGCAGCTCCCGATCCGCACGGCCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGCATGGTGTTGTTCCGAGGCATGCCGCTCAATTGGTAGAGAGCAGAAGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

TCCCTCGAGGCCTTCCTCCCCACCGGTTCAGCAGCTCCCGATCCGCACGGCCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGCATGGTGTTGTTCCGAGGCATGCCGCTCAATTGGTAGAGAGCAGAAGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

TCCCTCGAGGCCTTCCTCCCCACCGGTTCAGCAGCTCCCGATCCGCACGGCCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGCATGGTGTTGTTCCGAGGCATGCCGCTCAATTGGTAGAGAGCAGAAGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

TCCCTCGAGGCCTTCCTCCCCACCGGTTCAGCAGCTCCCGATCCGCACGGCCAAAGGCCGATTCGCGCTCCTCCAGCCTTCCTCCGCGTCCAACAGCAAGgtgattagtt ... gcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGCATGGTGTTGTTCCGAGGCATGCCGCTCAATTGGTAGAGAGCAGAAGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgatttcaccagttttacaatcatgtctcattctcatgatgtgcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGCATGGTGTTGTTCCGAGGCATGCCGCTCAATTGGTAGAGAGCAGAAGCCT
 ccctgat  putative branch site (score: 100)
               ttttacaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgcctgctgattctgagcctttattatctgcactgatcttcccctgatttcaccagttttacaatcatgtctcattctcatgatgtgcatatgcagTGAAAAACTTCAACCCAAGAATGGCGATGTCTTGGACAAGAGGGTTAAAGCATGGTGTTGTTCCGAGGCATGCCGCTCAATTGGTAGAGAGCAGAAGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - cctgctg
- - - - - - - - - - - - - - - tctgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgatgt