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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatcttgaaggcactactatctgtttctgtgattgttaattttagtaggatatagtctgaccacattgtattgttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG

Basic information

species Zea mays
transcript GRMZM2G050961_T06
intron # 2
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|166409968|gb|EG192262.1|EG192262
EST:     CTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTT
genomic: CTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTT
EST: gi|211349701|gb|FL449949.1|FL449949
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|13198326|gb|BG354265.1|BG354265
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|19058136|gb|BM736803.1|BM736803
EST:     TGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|6342692|gb|AW165516.1|AW165516
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|166483222|gb|EG111081.1|EG111081
EST:     CCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATAGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGT
genomic: CCAAAATCTGCTGTTAAGTTTGAGAGATATCTGAT-GGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGT
EST: gi|13249748|gb|BG360653.1|BG360653
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCT-GGAA-AAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|6431818|gb|AW172022.1|AW172022
EST:     AAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGNGAAGTTGAGGCTGGGAAGAAG
genomic: AAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|211485848|gb|FK973440.1|FK973440
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG

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), 48 (downstream exon)
Score: 387

AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 781

AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 282

AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 437

AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgattgttaattttagtaggatatagtctgaccacattgtattgttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
                          gtctgac  putative branch site (score: 437)
     tgttaattttagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatcttgaaggcactactatctgtttctgtgattgttaattttagtaggatatagtctgaccacattgtattgttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG