Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACGTCGAGAGGATTTGTTGAAGAAGATTTCGCTAAAGTTGCTGACTTCTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaagtcttggttttttctccctaagaaaacaaaccacagtgactgttttagatgcatttgcattcgttgaggtgtccttatcactagttggatgatctgatttatgttttgtttttaattcttgcaatttag

Basic information

species Zea mays
transcript GRMZM2G135283_T03
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os03g52840.3 (Oryza sativa), 5'ss of exon 11
---CTTACGTCGAGAGGATTTGTTGAAGAAGATTTCGCTAAAGTTGCTGACTTCTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaagtcttggttttttctccctaagaaaac----aaaccacagtgactgttttagatgcatttgcattcgttgaggtgtccttatcactagttggatgatctgatttatgttttgtttttaattcttgcaatttag
   || || || |||||||||||||| || || || ||||| |||||||| ||||||||||||||||||||  |||| |||||| ||||||||||| |   |||||  ||||| || | ||||||| |   |  |||||     | |  |||       | ||  |||||||    | |  | |  ||    | ||||   | |||| |||  ||| ||  |||  ||||    ||||||||||||
GCACTGACCTCAAGAGGATTTGTTGAGGAGGACTTTGCTAAGGTTGCTGATTTCTTCGATGCAGCAGTGAACTTGGCTTTGAAGGTTAAGGCTGCAGC---AGgtctgtcaaattcctagttttttttttgtttgaaaatgttgagaatacaaaacaattgttgcatgcattgaggtgccctcatatgatact-tcaccc-taggatcatcgtattcatcattttgtttttccccttgcaatttag

upper sequence: GRMZM2G135283_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA18G27710.1 (Glycine max), 5'ss of exon 15
CTTACGTCGAGAGGATTTGTTGAAGAAGATTTCGCTAAAGTTGCTGACTTCTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcact----caaagtcttggttttttctccctaagaaaacaa--accacagtgactg--------ttttagatgcatttgcattcgttgaggtgtccttatcactagttggatgatctgatttatgttttgtttttaattcttgcaatttag
||||| || |||||||||||||| || ||||| | ||| || || || ||||| ||||||||||||||  ||||  ||||||||||||     |  | ||||   |    |  ||   |   || | || ||| ||    |        |  |  |||        |  || ||  ||||  | |  ||   ||   ||| |     | |   | | || || | || ||  | || || | ||  |||    
CTTACTTCTAGAGGATTTGTTGAGGAGGATTTTGTTAAGGTAGCAGAGTTCTTTGATGCAGCAGTGAAGTTGGCTGTGAAGATTAAGGGACAGAGCAAAGgttcttacttcttagatcttcattatgcttcctgagtttgcgtttgtttctttatctgaaaatgactcataaat-tattttaacttctttctgttggcttgttgggtgcttactaagctaatatgtggttgatgttgaaattttttaatcag-
















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|113703934|gb|EE681438.1|EE681438
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|148973318|gb|EE024403.2|EE024403
EST:     TTTCGATGCAGCAGTGAATTTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATTTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|6194529|gb|AW146633.1|AW146633
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|60352787|gb|DN219760.1|DN219760
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|67017024|gb|CO445773.1|CO445773
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|60344488|gb|DN211461.1|DN211461
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|108953686|gb|EC364842.1|EC364842
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|71299009|gb|DR785497.1|DR785497
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|32867520|gb|CF007202.1|CF007202
EST:     GAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: GAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|60354435|gb|DN221408.1|DN221408
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|60343439|gb|DN210412.1|DN210412
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|40336482|gb|CK370552.1|CK370552
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|113700941|gb|EE678445.1|EE678445
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|32850232|gb|CD989913.1|CD989913
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|6102053|gb|AW126523.1|AW126523
EST:     TTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|67013913|gb|CO442662.1|CO442662
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|37393418|gb|CF633973.1|CF633973
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|60397906|gb|DN230722.1|DN230722
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|14204327|gb|BG838004.1|BG838004
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|211502770|gb|FL432440.1|FL432440
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|5804699|gb|AI979669.1|AI979669
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|6449712|gb|AW181252.1|AW181252
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|148945830|gb|EC891119.2|EC891119
EST:     TTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|37391313|gb|CF632898.1|CF632898
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|211373639|gb|FL261168.1|FL261168
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|60357206|gb|DN224179.1|DN224179
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|89249961|gb|DY621747.1|DY621747
EST:     TTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|5915216|gb|AW052857.1|AW052857
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCCCTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
EST: gi|60353152|gb|DN220125.1|DN220125
EST:     CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAG                         GTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC
genomic: CTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaa ... tgcaatttagGTGGAACAAAGCTGAAGGACTTTGTTGCCACTTTGCAATCTGATAGCATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACGTCGAGAGGATTTGTTGAAGAAGATTTCGCTAAAGTTGCTGACTTCTTCGATGCAGCAGTGAATCTGGCCTTGAAGATTAAGGCTGCAACGACAGgtcactcaaagtcttggttttttctccctaagaaaacaaaccacagtgactgttttagatgcatttgcattcgttgaggtgtccttatcactagttggatgatctgatttatgttttgtttttaattcttgcaatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA