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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactggatcgacagctccaagctcattccatgatttcgatctcgcttgtgtactgtactcgggcctggagcttgttctgatccgatcctgccttcctgctcggcgcccgcccgccccacttattcgattccatctcgtgttcctctgtgctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG

Basic information

species Zea mays
transcript GRMZM2G108849_T01
intron # 1
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|211436682|gb|FL284630.1|FL284630
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCG-A-MRAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|13177948|gb|BG349206.1|BG349206
EST:     GGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211436681|gb|FL284629.1|FL284629
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCG-A-MRAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211439281|gb|FL284648.1|FL284648
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCGAMG-AAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211439276|gb|FL284643.1|FL284643
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211436678|gb|FL284626.1|FL284626
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCGAMG-AAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211439282|gb|FL284649.1|FL284649
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211439272|gb|FL284639.1|FL284639
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCG-A-MRAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211436674|gb|FL284622.1|FL284622
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCG-AMRAAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211439275|gb|FL284642.1|FL284642
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCGAMG-AAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211439277|gb|FL284644.1|FL284644
EST:     CGTTGGCCGAAGAAGAGGAGAAGCG-A-CVRAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: CGTTGGCCGAAGAAGAGGAGAAGCGAAGC-AAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211436686|gb|FL284634.1|FL284634
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCGAMG-AAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211439269|gb|FL284636.1|FL284636
EST:     GCGTTGGCCGAAGAAGAGGAGAAGCG-A-VRAGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: GCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
EST: gi|211436679|gb|FL284627.1|FL284627
EST:     CGTTGGCCGAAGAAGAGGAGAAGCGAMG-AANGCAGGCTTCGAGAACAAG                         GGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG
genomic: CGTTGGCCGAAGAAGAGGAGAAGCGAAGCAA-GCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCG

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), 40 (downstream exon)
Score: 72

CTATATATATAATACACACACTAGTGTAGTAGTGTGGAGTACTTCAATTGGCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 132

CTATATATATAATACACACACTAGTGTAGTAGTGTGGAGTACTTCAATTGGCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

CTATATATATAATACACACACTAGTGTAGTAGTGTGGAGTACTTCAATTGGCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

CTATATATATAATACACACACTAGTGTAGTAGTGTGGAGTACTTCAATTGGCGTTGGCCGAAGAAGAGGAGAAGCGAAGCAAGCAGGCTTCGAGAACAAGgtactggatc ... gctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcccgcccgccccacttattcgattccatctcgtgttcctctgtgctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG
              acttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactggatcgacagctccaagctcattccatgatttcgatctcgcttgtgtactgtactcgggcctggagcttgttctgatccgatcctgccttcctgctcggcgcccgcccgccccacttattcgattccatctcgtgttcctctgtgctgctgcagGGGGAGGGGGAGGACCAAGCGAAAGGGGGAACTAGAGCAAGATGGGCGGCGAACTGCTGCTTGCGCTCCTCCTCGTCTCTGCTGCTGCCGCCCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC