Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgctagcttatgatgtcgttcaaaatgacattggagatgtgatgagtccagacttataaccttggcattcttatatgataatgttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAGGAAGCTGCTGTTGCCCCTGAGTTTGCCGCAATCACTGATTACCAAGGAG

Basic information

species Zea mays
transcript GRMZM2G126821_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126821_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g08440.1 (Oryza sativa), 3'ss of exon 3
gtatgatgctagcttatgatgtc--gttcaaaatgacattggagatg---tgatgagtccagacttataaccttggcattcttata---tgataatgttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAGGAAGCTGCTGTTGCCCCTGAGTTTGCCGCAATCACTGATTACCAAGGAG---
     ||||    |||| |  ||  |  ||   ||||||||||  ||   | ||||    |   | ||| |||| | || ||||||   |||  ||||  ||||||||| ||| |||| |||||||| ||||| ||||| || ||||||||||||||||||||| | |   | |  || ||||| || ||||||||||||   | |    
---gtatgcggtgttattacttcaagaacacgttgacattggaagtgcattcatgaagataatttcatatcctttgtatgcttatacactgagtatgtcttttgcagGTTGATCTGTTTTTCTACAGAGACCCTGAGGAGGCCAAGGAGCAGGAGGAGGAAGCTCCAG---CACAAGACTTTGCTGCCATCACTGATTACACCGCACCTG
















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|33101681|gb|CF061641.1|CF061641
EST:     TCTGCAGATGAGGGGCACTATCCTCCCTGGGCACCAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCGGGAGGAG
genomic: TCTGCAGATGAGGGGCACTATCCTCCCTGGGCAC-AAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|30306590|gb|CD001263.1|CD001263
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|32850981|gb|CD990662.1|CD990662
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTTGATCTGTTCTTCTACAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|30307128|gb|CD001801.1|CD001801
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|211208070|gb|FL437181.1|FL437181
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|6538929|gb|AW225068.1|AW225068
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|31362453|gb|CD446810.1|CD446810
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|110481295|gb|EE011014.1|EE011014
EST:     TCTGCAGATGAGGGGCACTATCCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTTTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TCTGCAGATGAGGGGCACTAT-CCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|5510808|gb|AI857192.1|AI857192
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|211518207|gb|FL037244.1|FL037244
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|30307129|gb|CD001802.1|CD001802
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|211540690|gb|FL218505.1|FL218505
EST:     TCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATNG                         GTGGGTTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGA
genomic: TCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCAT-Ggtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGA
EST: gi|30032245|gb|CB834096.1|CB834096
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|61118621|gb|DN559582.1|DN559582
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|32849968|gb|CD989649.1|CD989649
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTTGATCTGTTCTTCTACAGAGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|18964153|gb|BM660841.1|BM660841
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GNGGATTGGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|60351487|gb|DN218460.1|DN218460
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|149014517|gb|EE044146.2|EE044146
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|211211019|gb|FL456131.1|FL456131
EST:     TTCTGCARATGAGGGGCACTATCCTCCCTGGGCMCAAGTGGGAGGTCATG                         GTGGATTTGTTYTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|19770436|gb|BQ035157.1|BQ035157
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|28987078|gb|CB351453.1|CB351453
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|29543918|gb|CB604298.1|CB604298
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|24768430|gb|CA403559.1|CA403559
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|60351254|gb|DN218227.1|DN218227
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|12972713|gb|BG268119.1|BG268119
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCCAGAGGAAGCAAAGGAGCAGGAGGA
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCC-AGAGGAAGCAAAGGAGCAGGAGGA
EST: gi|21330457|gb|BQ485838.1|BQ485838
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCA
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCA
EST: gi|83279186|gb|DV943194.1|DV943194
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTAGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
EST: gi|31353712|gb|CD438069.1|CD438069
EST:     TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATG                         GTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG
genomic: TTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgct ... ttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgagtccagacttataaccttggcattcttatatgataatgttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAGGAAGCTGCTGTTGCCCCTGAGTTTGCCGCAATCACTGATTACCAAGGAG
               ttataac  putative branch site (score: 2)
                            attcttatatgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgctagcttatgatgtcgttcaaaatgacattggagatgtgatgagtccagacttataaccttggcattcttatatgataatgttgtttgcagGTGGATTTGTTCTTCTACAGGGACCCAGAGGAAGCAAAGGAGCAGGAGGAGGAAGCTGCTGTTGCCCCTGAGTTTGCCGCAATCACTGATTACCAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG