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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgtttatatgttcagatgacaacgctattcatgccactccatctcacatgctaattactccaccaggctcataacaaaacactgtttatatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG

Basic information

species Zea mays
transcript GRMZM2G081848_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g07310.3 (Oryza sativa), 3'ss of exon 3
--cattgtttatatgttcagatgacaacgctattcatgccactccatctcacatgctaattactccaccaggctcataacaaaacactg-----tttatatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG
   | |  ||  |||||  || ||    | |||      ||||||| ||  ||  ||||  ||| ||||| | ||||   ||||  |||     | | | | ||||||||||||||||||| ||||| ||||| ||||||||||| ||||| ||||||||||||||||| |||||
taaacttattgcatgttgtga-gatgcagttat------cactccaccttgcacactaaccactgcaccaaggtcatgctaaaatgctgaatgctctttgttttcagATGACAAAGCTGGCAATTATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG

upper sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 4
cattgtttatatgttcagatgacaacgctattca-tgccactccatctcaca-tgctaattactccaccaggctcataacaaaacactgtttatatg----ttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG
   |||||  || ||     |||    ||||| | ||   |   || | | | |  |||||   || | |  ||  | | |  || || ||  | |     | ||||||||||| ||||| || || |||||||||||| | ||||| ||||||||||| ||||||| ||| ||
-tctgtttgaatttt-----gactcttctatttagtgtttcagaattttataattttaattttgcctctaaacttctgatattactctcttggttttgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAG

upper sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 4
------------------cattgtttatatgttcagatgacaacgctattcatgccactccatctcacatgctaattactccaccaggctcataacaaa----acactgtttatatgttc-agATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG
                   ||  |   ||   | | |||   |  || ||  | |    |||| |||  || |  | |    |   |  ||  |||  |    | | ||||| | | ||| |||||||||||||||| || ||||||||||||||  |  |||||||||||||||||||||||||||| ||
gtaaaattaattcttctgaatattccctactattacatgttca-acttttggtcctttgccatttca-gtgtttctcaagagagtggtttctgaacttatgttatattgtttgtgtattccagATGACAAAGCTGGCAATCATTCCCTGTACTGTACTCTTGGAGACCCTTTTCTTCAGGAAGAAATTCAG

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|101387228|gb|EB815631.1|EB815631
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGG
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGG
EST: gi|89251400|gb|DY623186.1|DY623186
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|148991600|gb|EE033131.2|EE033131
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCCGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAG
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAG
EST: gi|148967838|gb|EE019130.2|EE019130
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|148960883|gb|EE011564.2|EE011564
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|148932303|gb|EC875882.2|EC875882
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|148997312|gb|EE035807.2|EE035807
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|149012667|gb|EE042641.2|EE042641
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTT
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTT
EST: gi|50322320|gb|CO517446.1|CO517446
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|149110398|gb|EE190395.2|EE190395
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|31358400|gb|CD442757.1|CD442757
EST:     TTGGACTTCTTAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|71328578|gb|DR800947.1|DR800947
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|148936002|gb|EC880058.2|EC880058
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|149102837|gb|EE288179.2|EE288179
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|149105555|gb|EE291088.2|EE291088
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|87152152|gb|DY396941.1|DY396941
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|148995261|gb|EE034502.2|EE034502
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
EST: gi|149097659|gb|EE183556.2|EE183556
EST:     TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAG                         ATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC
genomic: TTGGACTTCTAAACTTGAGTTTGGGTTTCAATTCTGTTGGTTTCTATCAGgtacacatcc ... atatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcacatgctaattactccaccaggctcataacaaaacactgtttatatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG
                          tcataac  putative branch site (score: 2)
                                          tttatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgtttatatgttcagatgacaacgctattcatgccactccatctcacatgctaattactccaccaggctcataacaaaacactgtttatatgttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA