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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcagagccgctctatctactcggtatcagtatcaccgatctggttctcgattcggttgctaattcacagttcctgtgctggtggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAGGAGGAGTAGAGTTTGCACCAAAAGTTACCCTGCTGCTGCTAGAGCTTGG

Basic information

species Zea mays
transcript GRMZM2G047143_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047143_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g40940.2 (Oryza sativa), 3'ss of exon 4
gtatagcagagccgctctatctactcggtatcagtatcaccgatctggttctcgattcggttgctaat-tcacagttcctgtgctggtggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAGGAGGAGTAGAGTTTGCACCAAAAGTTACCCTGCTGCTGCTAGAGCTTGG--
       |    | ||  ||| |||| || ||  | |   ||  |||  ||||     | ||||| |  | ||||  || ||| |  ||   ||||||||||| |||||||||||||| || || ||||||   |||||||||||||||||| ||   ||    |     | |||       ||  |      |      
----gtgaatatcactgaatcgactccgtttcttttttttcg--ctgcctctc--ccagattgctgacgttacagcgcc-gtgttcttgccatggcagATTCACAAGGTGGACACGCTCGTCTCCTACAAGGTCGACGAGTGGGACGAGGAGTAG--AAGCCGCCGGTGGAGGTTGGAGCCATGAGGAGGAGACCCCCTT
















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|31406271|gb|CD485003.1|CD485003
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|161589516|gb|EY961313.1|EY961313
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGC
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGC
EST: gi|76018768|gb|DT945938.1|DT945938
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|76019513|gb|DT946683.1|DT946683
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACCCCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|78108572|gb|DV526990.1|DV526990
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|34391357|gb|CF384585.1|CF384585
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGGGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|101396573|gb|EB820212.1|EB820212
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|31997662|gb|CD661703.1|CD661703
EST:     AGCTCATCGAAAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|211015021|gb|FL312920.1|FL312920
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|91054081|gb|EB164499.1|EB164499
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|87155980|gb|DY400769.1|DY400769
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|31441067|gb|CD510498.1|CD510498
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|101396571|gb|EB820211.1|EB820211
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTCCAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|91054064|gb|EB164482.1|EB164482
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|31664270|gb|CD572995.1|CD572995
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|211437588|gb|FL436643.1|FL436643
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|148946894|gb|EC892174.2|EC892174
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|78078551|gb|DV506963.1|DV506963
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTTCAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|5713718|gb|AI943710.1|AI943710
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|60349178|gb|DN216151.1|DN216151
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|45847234|gb|CN071177.1|CN071177
EST:     CGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGAACGAG
genomic: CGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|78023687|gb|DV492074.1|DV492074
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|12969132|gb|BG266077.1|BG266077
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|91873923|gb|EB403880.1|EB403880
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|4966592|gb|AI691448.1|AI691448
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
EST: gi|32912163|gb|CF016975.1|CF016975
EST:     AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAG                         ATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG
genomic: AGCTCATCGACAACCCGCAGATGGTTAAGCTGCACTCCTTCGACACCAAGgtatagcaga ... ggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctggttctcgattcggttgctaattcacagttcctgtgctggtggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAGGAGGAGTAGAGTTTGCACCAAAAGTTACCCTGCTGCTGCTAGAGCTTGG
                   tgctaat  putative branch site (score: 2)
                      taattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagcagagccgctctatctactcggtatcagtatcaccgatctggttctcgattcggttgctaattcacagttcctgtgctggtggagtggcagATTCATAAGGTGGACACGCTGGTGTCGTACAAGAAGGACGAGTGGGACGAGGAGGAGTAGAGTTTGCACCAAAAGTTACCCTGCTGCTGCTAGAGCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT