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

...atgtaaatactgaccatcaattgtctctcatccttgactttaggtgtttcagcaaacctttttatagtgttttgacaaacgttgttttgcatttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCCAAAATTTGGGTATCGAATCAACTGATGAGGAGATAAAAGATCTTTTTGA

Basic information

species Zea mays
transcript GRMZM2G142693_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142693_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10470.1 (Oryza sativa), 3'ss of exon 2
--atgtaaatact-gaccatcaattgtctctcatccttgactttaggtgtttcagcaaacctttttatagtgttttgacaaacgttgttttgcatttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCCAAAATTTGGGTATCGAATCAACTGATGAGGAGATAAAAGATCTTTTTGA
   ||||   ||| |   |||     ||    |||  ||     |  |  ||   |     || || |  |||| |||||||  |  || ||  | | | |||||||||||||||||||||||||||||||||  ||||| |||| |||||| ||||| |||| ||||  ||  || ||||||||||||||||| || ||| |
aattgtattcacttggaaatc--ccatcctcgatctgtg-tggcatttcctttgtccccttttgttttcttgttctgacaaatatcattatgtttctctccagATGAAGATTCCAATGGTGAAATAGATCAACAAGAACTTAAGCATTGTTTTCAAAAGTTGGATATCTCATTCACAGATGAGGAGATAAAAGACCTATTTCA
















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|148949779|gb|EC895262.2|EC895262
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
EST: gi|211260869|gb|FL247908.1|FL247908
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
EST: gi|211263296|gb|FL247911.1|FL247911
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTC
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTC
EST: gi|211263294|gb|FL247909.1|FL247909
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
EST: gi|211263305|gb|FL247920.1|FL247920
EST:     AAAATCGACGAGAGTTTGAGAAACTNCCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
genomic: AAAATCGACGAGAGTTTGAGAAACTGC-AGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
EST: gi|211263302|gb|FL247917.1|FL247917
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAAATGGTGAAATAGATCAACTGG
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAA-TGGTGAAATAGATCAACTGG
EST: gi|71438786|gb|DR819836.1|DR819836
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
EST: gi|211263300|gb|FL247915.1|FL247915
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
EST: gi|67033577|gb|CO462326.1|CO462326
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
EST: gi|211263301|gb|FL247916.1|FL247916
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCC
EST: gi|211265738|gb|FL247926.1|FL247926
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGT
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAA-TGGTGAAATAGATCAACTGGAACTCAAGCGTTGT
EST: gi|211263304|gb|FL247919.1|FL247919
EST:     TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTG                         ATGAAGATTCCAATGGTGAAATAGATC
genomic: TAAAATCGACGAGAGTTTGAGAAACTGCAGGACTATCTTCCAGGAATTTGgtgagcttta ... atttatgcagATGAAGATTCCAATGGTGAAATAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcagcaaacctttttatagtgttttgacaaacgttgttttgcatttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCCAAAATTTGGGTATCGAATCAACTGATGAGGAGATAAAAGATCTTTTTGA
                        ttttgac  putative branch site (score: 3)
             tttttatagtgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtaaatactgaccatcaattgtctctcatccttgactttaggtgtttcagcaaacctttttatagtgttttgacaaacgttgttttgcatttatgcagATGAAGATTCCAATGGTGAAATAGATCAACTGGAACTCAAGCGTTGTTTCCAAAATTTGGGTATCGAATCAACTGATGAGGAGATAAAAGATCTTTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - -tactgac
- - - - - - - - - - - - - - - - - - - - - - tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg