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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcctgtttccgtttcccaacactcttcagctattccgccccgtgaggtgttcattttgggagtgacccgccgttgagaattcgtgcaatccgtgctgttttgattttcgaatgctctgctattgacgatacttcggttttgtttgctgtttcctgtttcaattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCGAAGCTGTGCGACCGAAACTTCGGCATTGGTGCCGACGGCGTCATCTTCG

Basic information

species Zea mays
transcript GRMZM2G130332_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130332_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g37960.1 (Oryza sativa), 3'ss of exon 1
----------------gtgcgcctgtttc-cgtttcccaacactcttcagctattccgccccgtgaggtgttcattttgggagtgacccgccgttgagaattcgtgcaatccgtgctgttttgatt--ttcgaatgctctgctattgacgatacttcggttttgtttgctgtttcctgtttcaattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCGAAGCTGTGCGACCGAAACTTCGGCATTGGTGCCGACGGCGTCATCTTCG
                | ||  |  |||| | ||||  |  ||   |  | |  | | |  |      | || ||       || | | | || |  |  | |  | |||  | || || |    |  ||   | ||  || | |      |  || | ||| || |    |||  | | |        |||||||||| ||||||||| | |||||||||||||||||||||||||| ||||||||||||||| | ||||||||| | || |||||||| || |||||||
gtgcgacgccttactagcgcttccatttcacttttcttagaaccgatttgttgcttcccttca-atttttttaatcccctttgtaatcagtcgcttcgtctgcacg-aattagagcagtctctgctgctttagacgcggtgatttctgtatttttttgatttagtcttggattttttttctt------cagGTGGACAATAGGGATTCGGCCGTGCCGAAGGTGACGCCGGAGGAGGCGGCGAAGCTGTGCGACAGGAACTTCGGCGTCGGCGCCGACGGTGTGATCTTCG
















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|148986800|gb|EE030596.2|EE030596
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|87155814|gb|DY400603.1|DY400603
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|91052902|gb|EB163320.1|EB163320
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|93014173|gb|EB639693.1|EB639693
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|91878422|gb|EB408379.1|EB408379
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|211442704|gb|FL002346.1|FL002346
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGTATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCTGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|148961368|gb|EE012101.2|EE012101
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|71324621|gb|DR799009.1|DR799009
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|211442708|gb|FL002350.1|FL002350
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|91869787|gb|EB400540.1|EB400540
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACATGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|71769300|gb|DR967237.1|DR967237
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|78088914|gb|DV517307.1|DV517307
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|76286735|gb|DV026303.1|DV026303
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|78088792|gb|DV517185.1|DV517185
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|50337846|gb|CO532972.1|CO532972
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|22133843|gb|BQ833933.1|BQ833933
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|71329026|gb|DR801212.1|DR801212
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|26558147|gb|CA830382.1|CA830382
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|22715577|gb|BU197842.1|BU197842
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|211442703|gb|FL002345.1|FL002345
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|211508993|gb|FL162734.1|FL162734
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|76014966|gb|DT942136.1|DT942136
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|101395236|gb|EB819548.1|EB819548
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|148961806|gb|EE012586.2|EE012586
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|76915664|gb|DV166066.1|DV166066
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGA
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGA
EST: gi|71443835|gb|DR824885.1|DR824885
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|211442709|gb|FL002351.1|FL002351
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|26559567|gb|CA831802.1|CA831802
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|101383177|gb|EB813643.1|EB813643
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|148970899|gb|EE021693.2|EE021693
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|74233526|gb|DT641440.1|DT641440
EST:     GCGCTCTCCACTTCGTCAAGT-CCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|211442702|gb|FL002344.1|FL002344
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
EST: gi|76017579|gb|DT944749.1|DT944749
EST:     GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG
genomic: GCGCTCTCCACTTCGTCAAGTACCAGGGCCTCGGCAATGACTTCATTATGgtgcgcctgt ... caattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgctattgacgatacttcggttttgtttgctgtttcctgtttcaattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCGAAGCTGTGCGACCGAAACTTCGGCATTGGTGCCGACGGCGTCATCTTCG
      tattgac  putative branch site (score: 2)
                                ctgtttcctgtttc  putative PPT
                       ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgcctgtttccgtttcccaacactcttcagctattccgccccgtgaggtgttcattttgggagtgacccgccgttgagaattcgtgcaatccgtgctgttttgattttcgaatgctctgctattgacgatacttcggttttgtttgctgtttcctgtttcaattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCGGAGGAGGCCGCGAAGCTGTGCGACCGAAACTTCGGCATTGGTGCCGACGGCGTCATCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG