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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttcgatcatttatttatcaaaggaatgcattcatgattaagcgaccggtatgtttctgtttctcacttcacttgttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCGGCAGGGATCTTCAAGCTGCTCGTGTTACAGCAG

Basic information

species Zea mays
transcript GRMZM2G100652_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100652_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 5
gtaagttttcgatcatttatttatcaaaggaatgcattcatgattaagcgaccggtatgtttctgtttctcacttcacttgttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCGGCAGGGATCTTCAAGCTGCTCGTGTTACAGCAG
||||| || |   ||| |   |||    |  |  | || |   | |  | | |    || | |  ||||||||| |         | | ||||||||||||||||||||| || ||||||||||||||||| ||||||||||||| ||||||||||||||| |||||||||||||
gtaagcttccagccatgt-cctat-gcggatacacctttacattaatactagccaactgatgc-atttctcactcc---------ccaaagAATTCTTGCACCGAGCTGCGGATCTCACACTGGTACCATCAGTTGCTATCGGCAAGGATCTTCAAGCTGCCCGTGTTACAGCAG

upper sequence: GRMZM2G100652_T03 (Zea mays), 3'ss of exon 4
lower sequence: EFJ29760 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttttcgatcatttatttatcaaaggaatgcattcatgatt--aagcgaccggtatgtttctgtttctcacttcacttgttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCGGCAGGGATCTTCAAGCTGCTCGTGTTACAGCAG
                         ||||     | |||   |    || | |  | ||  ||| | |     ||||    ||| |  |  |||||||||||| |||||||||||||| || |||||| | ||   || | | || |  || ||  |||| ||| | |   || |||
-----------------------gtaaagtttcactttcccaagccaaatcaaatgttaattttttttaaaaaactttttctgtcg--tgcagAATTCTTGCATCGAGCTGCAGACCTTACGCTGGTAACTTCCAGTGTTCTTGGAAAAGAGCTCAAAGCAGCTGGCGCAGCAACAG
















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|67042909|gb|CO469164.1|CO469164
EST:     ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAA                         AATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTAT
genomic: ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAAgtaagttttc ... ttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTAT
EST: gi|71425523|gb|DR806728.1|DR806728
EST:     CTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAA                         AATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
genomic: CTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAAgtaagttttc ... ttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
EST: gi|78076032|gb|DV504466.1|DV504466
EST:     ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAA                         AATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
genomic: ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAAgtaagttttc ... ttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
EST: gi|87156413|gb|DY401202.1|DY401202
EST:     ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAA                         AATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
genomic: ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAAgtaagttttc ... ttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
EST: gi|26560034|gb|CA832269.1|CA832269
EST:     ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAA                         AATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTG
genomic: ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAAgtaagttttc ... ttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTG
EST: gi|91869857|gb|EB400576.1|EB400576
EST:     ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAA                         AATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
genomic: ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAAgtaagttttc ... ttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
EST: gi|148981111|gb|EE027429.2|EE027429
EST:     ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAA                         AATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
genomic: ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAAgtaagttttc ... ttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
EST: gi|22935606|gb|BU571881.1|BU571881
EST:     ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAA                         AATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
genomic: ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAAgtaagttttc ... ttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
EST: gi|89762164|gb|DY689888.1|DY689888
EST:     ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAA                         AATTCTTGCACCGAGCT
genomic: ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAAgtaagttttc ... ttggctatagAATTCTTGCACCGAGCT
EST: gi|86473030|gb|DY239400.1|DY239400
EST:     ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAA                         AATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG
genomic: ACCCAGATATACTTTCAGCTGGCTTGTCAAGCCCATGTGGCTAATAATAAgtaagttttc ... ttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgattaagcgaccggtatgtttctgtttctcacttcacttgttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCGGCAGGGATCTTCAAGCTGCTCGTGTTACAGCAG
                              ttctcac  putative branch site (score: 2)
                   tatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttcgatcatttatttatcaaaggaatgcattcatgattaagcgaccggtatgtttctgtttctcacttcacttgttggctatagAATTCTTGCACCGAGCTGCAGACCTCACACTGGTACCATCTGTTGCTATCGGCAGGGATCTTCAAGCTGCTCGTGTTACAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT