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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgatcccctgaccagtctagctgccatttagttgcatccaacatcctaacgtgcttctgttttcaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAAGA

Basic information

species Zea mays
transcript GRMZM2G033526_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 4
gttagttgatc---ccctgaccagtctagctgccatttagttgcatccaacatcctaacgtgcttctgttttcaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAAGA
||  ||||||    || | ||  ||  | |  | |  |||||     ||| || || || | |||||| ||| ||||||||| |||||||| |||||||| |||||||| ||||| ||||||||||||||||| |||||||||||||||||||| |||||||| |||||| | || ||
gtcggttgatttctccataacatgttcaacctctagatagttatgcacaagatgctgacatccttctgcttt-aacagAGAAAGATTGGGAGGACATAAAGTTTGGTGTTGAAAATGGTGTTGATTTCTATGCCGTTTCCTTTGTGAAGGATGCAAAAGTTATTCATGAACTGAAGGA

upper sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------gttagttgatcccctgaccagtctagctg--ccatttagttgcatccaac--atcctaacgtgcttctgttttca-acagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAAGA
                  ||     ||  | ||        ||||   | | | |  ||  |   |    |  ||   || || |   | ||  |||| || ||||||||||||||||||||||| || || |||   || |||||||| || || |||||||| |||||||| |||||| ||||||| || ||  |
gttgataccagctgatgtttttccaatatcttgcatcaaggagcttttctaataaaatgtttttgagtggttatattctggttttaactccacgcagACAAAGATTGGGAAGACATAAAATTTGGAGTGGACAACCAAGTCGATTTCTACGCCGTCTCCTTTGTTAAGGATGCTAAAGTTGTCCATGAGTTGAAGAA

upper sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------------------------------gttagttgatcccctgaccagtctagctgccatttagttgcatccaacatcctaacgt-gcttctgt--tttcaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAAGA
                                                                                   ||  ||  ||  || ||  ||           | |     ||||||  |  |  | |  ||  |||  |||||||||| || || |||||||| || || ||||| || || |||   |||||||||||||| |||||||||||||| |||||  ||||  ||||||| || |||||
gttatcttttgttcttatgttttttctaataggtgattttctgtttctattttccacgaagttgatatgatgtttcttttacttttatttgtctacttacgtgttatttgaattgtaaaaaatatccaatcttttcccattactcatgtcatttcaacagACAAAGACTGGGAAGATATCAAGTTTGGAGTGGACAACCAAGTTGATTTCTATGCTGTTTCCTTTGTGAAAGATGCTGAAGTGGTCCATGAGTTGAAAGA

upper sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------gttagttgatcccctgaccagtctagctgccatttagttgc--atccaacatcctaacgtgcttctgttt------tcaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAAGA
                  | | |   ||    || |  |  |  |   || |     |  |      || | |  ||| |||  | |      ||  |||||||||||||||||||||| |||||||| || |||||    ||||||||||| ||  | || ||||| ||||| ||| | ||  | |||||  | |||  
aatttcattagtgtgcaatcactatctctagagatctatagaaattttatctgaacacggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC

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|13177889|gb|BG349072.1|BG349072
EST:     CGCCACCTAAATGTCCGTGGAAAGAGTGCTACTTCTGCCATCTATCACTG                         C
genomic: CGCCACCTAAATGTCCGTGGAAAGAGTGCTACTT-TGCCATCTATCACTGgttagttgat ... ttttcaacag-
EST: gi|13177889|gb|BG349072.1|BG349072
EST:     CGCCACCTAAATGTCCGTGGAAAGAGTGCTACTTCTGCCATCTATCACTG                         C
genomic: CGCCACCTAAATGTCCGTGGAAAGAGTGCTACTT-TGCCATCTATCACTGgttagttgat ... ttttcaacag-
EST: gi|211511544|gb|FL285063.1|FL285063
EST:     GCGCCACCTAAATGTCCGTGGAAAGAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACATAAA-TTTGGTGTCGAAAAACGGTGT-GATTTC
genomic: GCGCCACCTAAATGTCCGTGGAAAGAGTGCTACTTTGCCATCTATCACTGgttagttgat ... ttttcaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAA-CGGTGTTGATTTC
EST: gi|166473861|gb|EG141158.1|EG141158
EST:     GCGCCACCTAAATGTCCGTGGAAAGAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACAT
genomic: GCGCCACCTAAATGTCCGTGGAAAGAGTGCTACTTTGCCATCTATCACTGgttagttgat ... ttttcaacagAGAAGGATTGGGAAGACAT
EST: gi|67022089|gb|CO450838.1|CO450838
EST:     GCGCC-CCT-AATGTCCGTGGAAAGAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT
genomic: GCGCCACCTAAATGTCCGTGGAAAGAGTGCTACTTTGCCATCTATCACTGgttagttgat ... ttttcaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctagctgccatttagttgcatccaacatcctaacgtgcttctgttttcaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAAGA
                             tcctaac  putative branch site (score: 1)
                                       cttctgttttc  putative PPT
           atttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttgatcccctgaccagtctagctgccatttagttgcatccaacatcctaacgtgcttctgttttcaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG