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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcctaagaattccatttcttgcatccagaccgaaagccctgttgcttatgtttttaggtcgtgtttgttttaaccttcatccttcaattccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTGCTGGTTGGCCATGGCGCATGTAGAGCAGGCTCAGATCCTAGGTTTTTGG

Basic information

species Zea mays
transcript GRMZM2G143330_T01
intron # 7
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|166600634|gb|EG168678.1|EG168678
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACAAATCAGAG                         GCTGTTTGATTACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|7119030|gb|AW497573.1|AW497573
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAAACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|71760667|gb|DR958604.1|DR958604
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|7238210|gb|AW573477.1|AW573477
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAAACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|211472837|gb|FL449625.1|FL449625
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|101401499|gb|EB822429.1|EB822429
EST:     TTTTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|78086971|gb|DV515364.1|DV515364
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCGGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|32825463|gb|CD965185.1|CD965185
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACAAATCAGAG                         GCTGTTTGATTACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|74242276|gb|DT650190.1|DT650190
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|113606418|gb|DW775347.1|DW775347
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACC
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACC
EST: gi|74243657|gb|DT651571.1|DT651571
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACGGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|78087876|gb|DV516269.1|DV516269
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|5607833|gb|AI901500.1|AI901500
EST:     AATGTAGATAAAGAACAGACAAATCAGAG                         GCTGTTTGATTACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: AATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|78119407|gb|DV537791.1|DV537791
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|37374667|gb|CF623711.1|CF623711
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACAAATCAGAG                         GCTGTTTGATTACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|60353275|gb|DN220248.1|DN220248
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|32937077|gb|CF041896.1|CF041896
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACAAATCAGAG                         GCTGTTTGATTACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|166697734|gb|EG119427.1|EG119427
EST:     GCATCAAAATGTAGATAAAGAACAGACAAATCAGAG                         GCTGTTTGATTACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: GCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|91872572|gb|EB402529.1|EB402529
EST:     TTTTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|71301121|gb|DR786593.1|DR786593
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
EST: gi|31909651|gb|CD651025.1|CD651025
EST:     TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG                         GCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG
genomic: TTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTG

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), 49 (downstream exon)
Score: 305

CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTGCTGGTTGGCCATGGCGCATGTAGAGCAGGCTCAGATCCTAGGTTTTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTGCTGGTTGGCCATGGCGCATGTAGAGCAGGCTCAGATCCTAGGTTTTTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 151

CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTGCTGGTTGGCCATGGCGCATGTAGAGCAGGCTCAGATCCTAGGTTTTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAGgtaccacttc ... tccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTGCTGGTTGGCCATGGCGCATGTAGAGCAGGCTCAGATCCTAGGTTTTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttatgtttttaggtcgtgtttgttttaaccttcatccttcaattccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTGCTGGTTGGCCATGGCGCATGTAGAGCAGGCTCAGATCCTAGGTTTTTGG
                        ttttaac  putative branch site (score: 255)
                              ccttcatccttcaatt  CT-rich tract
                    tttgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcctaagaattccatttcttgcatccagaccgaaagccctgttgcttatgtttttaggtcgtgtttgttttaaccttcatccttcaattccttttcagGCTGTTTGATGACCAACCGGTTCAGTTTCTTGGTTCAGATGTTAGATGTTGCTGGTTGGCCATGGCGCATGTAGAGCAGGCTCAGATCCTAGGTTTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - -tgcatcc
- - - - - - - - - - - - - - - - - - - - ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - tgttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt