Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcagaaatatttggcagaggctcaatgcttttgcaagagattttaaagaaatctcaacagcgcttttacttctgctctacctttttgctctgtgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGCGGGTATAATCCCTACCATGGCTACCCTTATAGATCATATGGAGCACCGT

Basic information

species Zea mays
transcript GRMZM2G108919_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 4
gttcagaaatatttggcagaggctcaatgcttttgcaagagattttaaagaaatctcaaca-gcgcttttacttctgc--tctacc---tttttgctctgtgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGCGGGTATAATCCCTACCATGGCTACCCTTATAGATCATATGGAGCACCGT
|| |||||||      ||||  |    |   |   |   ||  || ||| |   ||   ||   | ||||      ||  | |||    ||| || | ||||||| |||||| || || |||||||||||||||||||||||||||||||||||||| || || || ||||| || ||||| ||||| |||||||| ||||| || || |
gtgcagaaattaccaacagatccctgttttgtcacctgaaggattcaaaaactccttttcacatgtttttgtcctcgcaatttactcaatttctgttttgtgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGTGGATACAATCCTTATCATGGTTACCCATATAGATCGTATGGGGCCCCAT
















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|7135303|gb|AW498018.1|AW498018
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|60351908|gb|DN218881.1|DN218881
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|211491424|gb|FL310090.1|FL310090
EST:     AGGAAGCTCTGAACTTGAATGAWTCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGAT
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGAT
EST: gi|211538316|gb|FL356780.1|FL356780
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAG-ACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|9731847|gb|BE510599.1|BE510599
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|211517204|gb|FL332921.1|FL332921
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|9731934|gb|BE510686.1|BE510686
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAATTAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|120480223|gb|EH210775.1|EH210775
EST:     AGGAAGTTTTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGATTAATGTCCCTGGGATGAAGCAGCGTCCCCCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|89247954|gb|DY619740.1|DY619740
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|9731848|gb|BE510600.1|BE510600
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|78085156|gb|DV513549.1|DV513549
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|84980134|gb|DW530483.1|DW530483
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|211289480|gb|FL348652.1|FL348652
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATSGAAGCAGCGTCCACCACG
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGAT-GAAGCAGCGTCCACCACG
EST: gi|84976804|gb|DW475226.1|DW475226
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|60399133|gb|DN231947.1|DN231947
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|6563947|gb|AW231569.1|AW231569
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCCCCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|31351934|gb|CD436291.1|CD436291
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCCTGGTCGACAGATTAAG                         GCTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACCC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|211110914|gb|FL481563.1|FL481563
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|50329632|gb|CO524758.1|CO524758
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGCCAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCCCCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|211177618|gb|FL479926.1|FL479926
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|31351939|gb|CD436296.1|CD436296
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|60399607|gb|DN232418.1|DN232418
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|31350541|gb|CD434898.1|CD434898
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|211279695|gb|FL337096.1|FL337096
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACCTAATGTCCCTGGGATGAAAGCAGCGTCCACCAC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGAC-TAATGTCCCTGGGATGAA-GCAGCGTCCACCAC
EST: gi|60394010|gb|DN226880.1|DN226880
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
EST: gi|211475451|gb|FL342194.1|FL342194
EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatctcaacagcgcttttacttctgctctacctttttgctctgtgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGCGGGTATAATCCCTACCATGGCTACCCTTATAGATCATATGGAGCACCGT
                                cctttttgctctgt  CT-rich tract
                ttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcagaaatatttggcagaggctcaatgcttttgcaagagattttaaagaaatctcaacagcgcttttacttctgctctacctttttgctctgtgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGCGGGTATAATCCCTACCATGGCTACCCTTATAGATCATATGGAGCACCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA