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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcagattgtacctctgtactcgattcatcctttcctgagctgcattttttttgtttatgaaaatacagtaggagccctggtaattcactaaagaagaaagagtaaaattaaagaaagaagggaaaccacacagctaatatgtgttcccaaatataatgattctgcatttcttaaatttgaaatgctttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATTCTGGAGGTTGGGTCAGATCTGTACTCAGCAATCATCGACGATAAGTTGT

Basic information

species Zea mays
transcript GRMZM2G422938_T01
intron # 11
splice site 3'
intron type U2

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|60344896|gb|DN211869.1|DN211869
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|28566570|gb|CB278218.1|CB278218
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGC
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGC
EST: gi|213188366|gb|FM182148.1|FM182148
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|50327383|gb|CO522509.1|CO522509
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|211528351|gb|FL435370.1|FL435370
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|31612367|gb|CD568989.1|CD568989
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|32835458|gb|CD975136.1|CD975136
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|8665543|gb|BE186359.1|BE186359
EST:     CTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: CTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|78022116|gb|DV490503.1|DV490503
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|71533581|gb|DR784340.1|DR784340
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|31405731|gb|CD484463.1|CD484463
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|50331880|gb|CO527006.1|CO527006
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|14244284|gb|BG842300.2|BG842300
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|5846767|gb|AI999850.1|AI999850
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|5762085|gb|AI967133.1|AI967133
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|45568059|gb|CK985881.1|CK985881
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|148947021|gb|EC892318.2|EC892318
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|211093394|gb|FL430975.1|FL430975
EST:     ATCACTTCTATGACCAGGGTGTSCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|4573048|gb|AI586697.1|AI586697
EST:     CCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: CCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|37394414|gb|CF634481.1|CF634481
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
EST: gi|211325068|gb|FL358359.1|FL358359
EST:     ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTG                         ATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT
genomic: ATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATT

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: 40 (upstream exon), 45 (downstream exon)
Score: 45

GGATATGCTTATATACTCACCCACCCTGGCATCCCCACGGTGTTCTATGATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATTCTGGAGGTTGGGTCAGATCTGTACTCAGCAATCATCGACGATAAGTTGT


Block sizes: 40 (upstream exon), 46 (downstream exon)
Score: 109

GGATATGCTTATATACTCACCCACCCTGGCATCCCCACGGTGTTCTATGATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATTCTGGAGGTTGGGTCAGATCTGTACTCAGCAATCATCGACGATAAGTTGT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 79

GGATATGCTTATATACTCACCCACCCTGGCATCCCCACGGTGTTCTATGATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATTCTGGAGGTTGGGTCAGATCTGTACTCAGCAATCATCGACGATAAGTTGT


Block sizes: 40 (upstream exon), 45 (downstream exon)
Score: 53

GGATATGCTTATATACTCACCCACCCTGGCATCCCCACGGTGTTCTATGATCACTTCTATGACCAGGGTGTGCCTCTCCATGACGAAATTGCTAAACTGgtacgcagat ... ttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATTCTGGAGGTTGGGTCAGATCTGTACTCAGCAATCATCGACGATAAGTTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcccaaatataatgattctgcatttcttaaatttgaaatgctttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATTCTGGAGGTTGGGTCAGATCTGTACTCAGCAATCATCGACGATAAGTTGT
                                           ctttttaccc  CT-rich tract
                             ttaaatttgaaatgct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcagattgtacctctgtactcgattcatcctttcctgagctgcattttttttgtttatgaaaatacagtaggagccctggtaattcactaaagaagaaagagtaaaattaaagaaagaagggaaaccacacagctaatatgtgttcccaaatataatgattctgcatttcttaaatttgaaatgctttttacccagATGCAAATCAGAAAATGCCAAGATATACATAGCCGTTCATCAATCAAAATTCTGGAGGTTGGGTCAGATCTGTACTCAGCAATCATCGACGATAAGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG