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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatatagtctgatcttttactttcactatatatatatatatatatatatatagtagaacccagttgcatacttggctatacacttaggacacgacactgtactagatatagtttcataagtctgcgaggatgttttttctgctctcatttctgaacctgatttgtactgatcgtgaaaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCACCTATGAGGACAGGGACGGGGACTGGATGCTTGTTGGAGATGTTCCCTG

Basic information

species Zea mays
transcript GRMZM2G142768_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142768_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g57250.2 (Oryza sativa), 3'ss of exon 2
gtaagtcatatagtctgatcttttactttcactatatatatatatatatatatatatagtagaacccagttgcatacttggctatacacttaggacacgacactgtactagatatagtttcataagtctgcgaggatgttttttctgctctcatttctgaacctgatttgtactgatcgtgaaaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCACCTATGAGGACAGGGACGGGGACTGGATGCTTGTTGGAGATGTTCCCTG
                                                                                               |   | | |||||    || |||  ||    | |   | |||   ||   |  |||  |   ||||||||| || |  | ||| |   | || ||||  | | ||||  | || || ||| |||||| |||  | || || ||||||||||| ||||||||||| || ||||||||||| |||||||||||||| ||
------------------------------------------------------------------------------------------ccatgcttcatattgtacctagta-agtcgcaagcttttttcatgataggttgattcatcttgtccatgaacctgaattatggttatcttcgcattt-tcagATAATACAAACTCGCTGAAACTACTAGACAACTCTGCCGAATACCAGCTCACCTACGAGGACAGGGATGGTGACTGGATGCTCGTTGGAGATGTTCCTTG
















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|76018364|gb|DT945534.1|DT945534
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|60399806|gb|DN232616.1|DN232616
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTATACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|71444561|gb|DR825611.1|DR825611
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|71437812|gb|DR818862.1|DR818862
EST:     GCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATC
genomic: GCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTT-GCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATC
EST: gi|149083987|gb|EE173375.2|EE173375
EST:     CATGTTCAGGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: CATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|91049936|gb|EB160354.1|EB160354
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|13198669|gb|BG354471.1|BG354471
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|50333994|gb|CO529120.1|CO529120
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|76924731|gb|DV170106.1|DV170106
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|71418902|gb|DR804585.1|DR804585
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCT
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCT
EST: gi|148961892|gb|EE012679.2|EE012679
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATT
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATT
EST: gi|78090139|gb|DV518513.1|DV518513
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|71301549|gb|DR786822.1|DR786822
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|71768772|gb|DR966709.1|DR966709
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|71433960|gb|DR815010.1|DR815010
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCNTAA-GCTATTAGACAGCTCATCGGAGTATCAGCTC
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTC-TAAAGCTATTAGACAGCTCATCGGAGTATCAGCTC
EST: gi|71768773|gb|DR966710.1|DR966710
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|60350167|gb|DN217140.1|DN217140
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|91050039|gb|EB160457.1|EB160457
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|71758859|gb|DR956796.1|DR956796
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|78114895|gb|DV533283.1|DV533283
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|113702671|gb|EE680175.1|EE680175
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|93011702|gb|EB637222.1|EB637222
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|78078295|gb|DV506710.1|DV506710
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCCAAGACTCTAAAGC
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGC
EST: gi|71433959|gb|DR815009.1|DR815009
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|149000117|gb|EE037243.2|EE037243
EST:     AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: AGCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
EST: gi|94477809|gb|EB706767.1|EB706767
EST:     GCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTA                         GCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA
genomic: GCACTTGAGCTCATGTTCATGAAGCCGTCCATTGGTCTTTGCACTTCTAgtaagtcata ... aaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttttctgctctcatttctgaacctgatttgtactgatcgtgaaaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCACCTATGAGGACAGGGACGGGGACTGGATGCTTGTTGGAGATGTTCCCTG
                                 tactgat  putative branch site (score: 2)
                                          tgaaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcatatagtctgatcttttactttcactatatatatatatatatatatatatagtagaacccagttgcatacttggctatacacttaggacacgacactgtactagatatagtttcataagtctgcgaggatgttttttctgctctcatttctgaacctgatttgtactgatcgtgaaaattatcagGCAGTTCAAAGACTCTAAAGCTATTAGACAGCTCATCGGAGTATCAGCTCACCTATGAGGACAGGGACGGGGACTGGATGCTTGTTGGAGATGTTCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG