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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccccccgcggccacgccgcctcgagcctagcgctcccatatgcctcaatcttccctgctcttcccatttacttgtttttttttcgcgattttgttttctacaagttccgtgctgattttcccccgtgcacgagtgttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAGGAGCGCAAGCGCAAGCGCGAGGCGCGCGAGGTGCACAGGC

Basic information

species Zea mays
transcript GRMZM2G174204_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 1
gtaagccccccgcggcc--------acgccgcctcgagcctagcgctcccatatgcctcaatcttccctgctcttcccattta--------------------cttgtttttttttcgcgattttgttttctacaagttccgtgctgatt---ttcccccgtgcacgagtgttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAGGAGCGCAAGCGCAAGCGCGAGGCGCGCGAGGTGCACAGGC
||||| ||||| || |          ||||||||| | |||  |    |    ||||    || |||| |   |  ||  | |                    |||    |||  |||   || |   || |     ||   |  |  ||   ||  | | || |||||| | |||||||||||||||||| ||||| ||||||||||||||||||||||||  |||||||||| |||||||||||||||||||||| | ||||||||||||||||| ||
gtaagtccccctcgccttctccccgccgccgcctccaacctgacctcactgcgtgcccagttcctcccgggattcaccgctgatcatctcagcacccgcgagtctttccgtttcctcgtcgttctcgctttttttttttttattttttttgagttttctcctggacgagt-tggctgcagCCGCAGGGAGATCACATAGAGCTTCACCAGAAGCGCCATGGCCGGCGCCTGGACTACGAGGAGCGCAAGCGCAAGCGGGCGGCGCGCGAGGTGCACAAGC
















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|78109120|gb|DV527537.1|DV527537
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211464729|gb|FL207495.1|FL207495
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211464737|gb|FL207503.1|FL207503
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211464734|gb|FL207500.1|FL207500
EST:     CTTTCCTCCTCAGCACCSAGNACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CTTTCCTCCTCAGCACCCA-AACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|14883663|gb|BI273476.1|BI273476
EST:     CCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|149079698|gb|EE168699.2|EE168699
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211464740|gb|FL207506.1|FL207506
EST:     CTTTCCTCCTCAGCACCCCAAACCCTGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CTTTCCTCCTCAGCA-CCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|15053622|gb|BI359167.1|BI359167
EST:     TTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: TTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211464732|gb|FL207498.1|FL207498
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211467266|gb|FL207509.1|FL207509
EST:     CCTTTCCTCCTCAGCACCCAATCCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|71440546|gb|DR821596.1|DR821596
EST:     CGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|148933462|gb|EC877158.2|EC877158
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211464728|gb|FL207494.1|FL207494
EST:     SCTTTCCTCCTCAGSACCCAAACCCCGACMTTCAGGGTTCCGCCGCCATG                         CCGCAGG-AGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|50332541|gb|CO527667.1|CO527667
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211462216|gb|FL207493.1|FL207493
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGG-AGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|22545768|gb|BU098142.1|BU098142
EST:     TTTCCTCCTCAGCACCCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCT
genomic: TTTCCTCCTCAGCA-CCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCA-GGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCT
EST: gi|31359359|gb|CD443716.1|CD443716
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGGCGCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCT
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGAC-CACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCT
EST: gi|211462211|gb|FL207488.1|FL207488
EST:     CCTTTCCTCCTCAGCACCCAATCCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211464730|gb|FL207496.1|FL207496
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|15313826|gb|BI478973.1|BI478973
EST:     CCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACGAGAAGCGCCATGGCAAGCGCCTG
genomic: CCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|211462214|gb|FL207491.1|FL207491
EST:     CCTTTCCTCCTCAGCACCCAATCCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|76917038|gb|DV166648.1|DV166648
EST:     CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CCTTTCCTCCTCAGCACCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
EST: gi|22819549|gb|BU499639.1|BU499639
EST:     CTTTCCTCCTCAGCACCCCAAACCCCGACCTTCAGGGTTCCGCCGCCATG                         CCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG
genomic: CTTTCCTCCTCAGCA-CCCAAACCCCGACCTTCAGGGTTCCGCCGCCATGgtaagccccc ... gttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttttctacaagttccgtgctgattttcccccgtgcacgagtgttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAGGAGCGCAAGCGCAAGCGCGAGGCGCGCGAGGTGCACAGGC
                    tgctgat  putative branch site (score: 3)
                       tgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccccccgcggccacgccgcctcgagcctagcgctcccatatgcctcaatcttccctgctcttcccatttacttgtttttttttcgcgattttgttttctacaagttccgtgctgattttcccccgtgcacgagtgttgctgcagCCGCAGGGAGACCACATCGAGCTTCACCAGAAGCGCCATGGCAAGCGCCTGGACCACGAGGAGCGCAAGCGCAAGCGCGAGGCGCGCGAGGTGCACAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG