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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttcttctcaattgaaacaaatatatccgctcccggcagttccaaagaaacttcttttggggtgctaagacatgtttttttaaccatcgtttccag

Basic information

species Zea mays
transcript GRMZM2G000393_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000393_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g08005.1 (Oryza sativa), 5'ss of exon 11
AGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttcttctcaattgaaacaaatatatccgctcccggcagttccaaagaaacttcttttggggtgctaagacatgtttttttaaccatcgtttccag
|| ||||| || ||||| |||||||||||||||||||||||||| |||||| | ||||| || ||||| ||||| ||||||||| ||||||| |||||||||| |   ||  |||   |||| | | |||  |  | |  | || |||  | |    | ||| |    ||||||  | |||  || |  |   ||| | |||
AGCTATGCCCATGATGACATATCAGTAGGTTCATGGATGATGGGGCTGAATACTACTTATGTTGATGACGACCGTTTGTGCTGCGGCAGTTCTAGACAAGgtaaaagctcgcctc--ctgaatccattat-cctaccctggacaattc--atggcggtacttcta---tgctaatgc-tgtaattctg-ctgccgtatgcag
















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|32928477|gb|CF033289.1|CF033289
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|166453596|gb|EG280202.1|EG280202
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGC
EST: gi|32846895|gb|CD986576.1|CD986576
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|211130920|gb|FL136658.1|FL136658
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTT
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTT
EST: gi|33091019|gb|CF051013.1|CF051013
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAGGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|74246238|gb|DT654152.1|DT654152
EST:     GCAACTTACGTGGATGATGACCGGTTGTGCTGC-GACAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: GCAACTTACGTGGATGATGACCGGTTGTGCTGCAG-CAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|32929367|gb|CF034179.1|CF034179
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|211130918|gb|FL136656.1|FL136656
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|4621425|gb|AI612258.1|AI612258
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTAC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|50334717|gb|CO529843.1|CO529843
EST:     TGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|166598258|gb|EG127937.1|EG127937
EST:     GGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: GGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|149005473|gb|EE040028.2|EE040028
EST:     TGCAACTTACGTGGATGATGCCCGGTTGTGCTGCAGCAGTTCCAGCCAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|24765385|gb|CA400544.1|CA400544
EST:     TGCAACTTACGTGGATGATGCCCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|50323552|gb|CO518678.1|CO518678
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|5124017|gb|AI745858.1|AI745858
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|45847888|gb|CN071831.1|CN071831
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGTAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|26557287|gb|CA829522.1|CA829522
EST:     TGCAACTTACGTGGATGATGCCCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|21828587|gb|BQ703271.1|BQ703271
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|110200892|gb|EC882789.1|EC882789
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATTTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|15082759|gb|BI389443.1|BI389443
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|113703856|gb|EE681360.1|EE681360
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

AGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGCTGTACATCCTGATGAAGATTTTGCACACCTGTCATTTTGTATACACTGC


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 49

AGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGCTGTACATCCTGATGAAGATTTTGCACACCTGTCATTTTGTATACACTGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 35

AGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGCTGTACATCCTGATGAAGATTTTGCACACCTGTCATTTTGTATACACTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 99

AGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGCTGTACATCCTGATGAAGATTTTGCACACCTGTCATTTTGTATACACTGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTATGCACACGATGATATATCAGTAGGTTCATGGATGATGGGACTGAATGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttcttctcaattgaaacaaatatatccgctcccggcagttccaaagaaacttcttttggggtgctaagacatgtttttttaaccatcgtttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG