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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaaatccagaaagacggttgatgtcctgtttctttttccttttatttttataaaccaaagaaacaacgaactggctgcccgtgttgctgactgtttccaaccctatctcgtctgcag

Basic information

species Zea mays
transcript GRMZM2G030784_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030784_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g05490.2 (Oryza sativa), 5'ss of exon 7
GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaaatccagaaagacggttgatgtcctgtttctttttccttttatttttataaaccaaagaaacaacgaactggctgcccgtgttgctgactgtttccaaccctatctcgtctgcag
| || ||||||| |||||||||||| ||||| |||||| |||||||||| ||||||||||| |||||||| ||||| |||||||||| ||| ||| |   || || || ||     |||       |  ||  |      | |  ||  |||   ||   ||  ||  |  ||||    |                           
GTTCCGTAACTGGTGCGAACTGCAAGGAGCTGGCAGCAAAGCCTGATGTTGATGGTTTTCTCGTCGGTGGTGCTTCATTGAAGgtaaagaataatacg--aacacagtagaacgattgtacagacatgatt--acccgcctgattcactgaat--accgtctccctttctttgttctgtag--------------------------
















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|71325325|gb|DR799341.1|DR799341
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAACGCGGCC
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCC
EST: gi|19437215|gb|BM953625.1|BM953625
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAACGCGGCCCCCGTGAAGTCCGCTTAA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
EST: gi|71323015|gb|DR798174.1|DR798174
EST:     CAGCACAGTCTGATGTCGATGGGTTTCTGGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATTCA-CGCGGCCACCCGTGAAGTCCG
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCAT-CAACGCGGCCACC-GTGAAGTCCG
EST: gi|67026065|gb|CO454814.1|CO454814
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGGTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTA
EST: gi|67024324|gb|CO453073.1|CO453073
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
EST: gi|71433477|gb|DR814527.1|DR814527
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAACGCGGGCACCGTGAAGTCTGCTTAA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
EST: gi|31355717|gb|CD440074.1|CD440074
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATC
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATC
EST: gi|67034586|gb|CO463136.1|CO463136
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGA-G                         CCTGAGTTCATCGACATCATCAACGCGGGCACCCGTGAA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACC-GTGAA
EST: gi|67016932|gb|CO445681.1|CO445681
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGA-G                         CCTGAGTT-ATCGACA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACA
EST: gi|38502719|gb|CF972579.1|CF972579
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAACGCCGGCCACCGTGAAGTCC
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGC-GGCCACCGTGAAGTCC
EST: gi|67012349|gb|CO441098.1|CO441098
EST:     AGCACAGCCTGATGTCAATGGTTTTCTTGTCCGG-GGAGCTTCTTTGAAG                         CCTGAGTTCATCTACTTCATCACCGCGGCCCCCGTGAA-TCCGCTTAA
genomic: AGCACAGCCTGATGTCGATGGTTTTCTTGTC-GGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
EST: gi|31355497|gb|CD439854.1|CD439854
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
EST: gi|29544034|gb|CB604414.1|CB604414
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAACGCGGCC-CCGTGAAGTCC-CTTA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTA
EST: gi|67020068|gb|CO448817.1|CO448817
EST:     AGCACAGCCTGATGTCGATGGTTTTNCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
genomic: AGCACAGCCTGATGTCGATGGTTTT-CTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
EST: gi|31354917|gb|CD439274.1|CD439274
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAA
EST: gi|67035472|gb|CO464005.1|CO464005
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTA
EST: gi|31355762|gb|CD440119.1|CD440119
EST:     CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAG                         CCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
genomic: CAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTTAA
EST: gi|67024408|gb|CO453157.1|CO453157
EST:     AGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTTCTT-GAAG                         CCTGAGTTCATCGACATCATCAACGCGGNCACCGTGAAGTCCGCTT
genomic: AGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTT-CTTTGAAGgtaatgaaaa ... tcgtctgcagCCTGAGTTCATCGACATCATCAACGCGGCCACCGTGAAGTCCGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTGTAACTGCTGCGAACTGCAAAGAGCTAGCAGCACAGCCTGATGTCGATGGTTTTCTTGTCGGTGGAGCTTCTTTGAAGgtaatgaaaaatccagaaagacggttgatgtcctgtttctttttccttttatttttataaaccaaagaaacaacgaactggctgcccgtgttgctgactgtttccaaccctatctcgtctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG