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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctactgttgttaactagtgtatgaagttcattgatgcatgatatctgagaaggttgcttgtttctatgatgtcttaatatttttgttttgtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG

Basic information

species Zea mays
transcript GRMZM2G120857_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 3
gctactgttgttaactagtgtatgaagttcattgatgcatgatatctgagaaggttgcttgtttctatgatgtcttaatat-----ttttgttttgtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG
           |  | ||||  |   | ||||   | |    ||| |     | |    ||| | ||| || ||||| | |     |||  |||||   |||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||||||| |||||||||||||| |||
----------gtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG

upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g16900.1 (Oryza sativa), 3'ss of exon 2
gctactgttgttaactagtgtatgaagttcattgatgcatgatatctgagaaggttgcttgtttctatgatgtcttaatat-----ttttgttttgtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG
        || |  | ||||  |   | ||||   | |    ||| |     | |    ||| | ||| || ||||| | |     |||  |||||   |||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||||||| |||||||||||||| |||
-----aaatggtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG

upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------gctactgttgttaactagtgtatgaagttcattgatgcatgatatctgagaaggttgcttgt-----ttctatgatgtc-ttaatattttt---gttttgtgat--ttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG
                                   | | |  ||  |   |  ||    || | |||| |  ||   || |   | | |   ||||     |||    || |  || ||| ||||   |||||||  |  | ||||| || |     || || ||||||||||| ||||||||||||||||| || || ||  | ||||| |||||| ||||||| ||||| |||||||| || |
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggcaattttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG

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|74239666|gb|DT647580.1|DT647580
EST:     TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
genomic: TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
EST: gi|148932534|gb|EC876336.2|EC876336
EST:     TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
genomic: TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
EST: gi|149101023|gb|EE187121.2|EE187121
EST:     TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
genomic: TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
EST: gi|148956957|gb|EC902897.2|EC902897
EST:     TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
genomic: TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
EST: gi|31358416|gb|CD442773.1|CD442773
EST:     TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
genomic: TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
EST: gi|76019791|gb|DT946961.1|DT946961
EST:     TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
genomic: TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
EST: gi|78109386|gb|DV527802.1|DV527802
EST:     TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
genomic: TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
EST: gi|149089409|gb|EE178649.2|EE178649
EST:     TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
genomic: TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
EST: gi|110201588|gb|EC883485.1|EC883485
EST:     TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAG                         GTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT
genomic: TCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGT

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: 47 (upstream exon), 48 (downstream exon)
Score: 213

GGCCGTGGCGCCGTTTTCAACGGAGTCCGGGGAGACCATTCGTGCCACGCTCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 474

GGCCGTGGCGCCGTTTTCAACGGAGTCCGGGGAGACCATTCGTGCCACGCTCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 462

GGCCGTGGCGCCGTTTTCAACGGAGTCCGGGGAGACCATTCGTGCCACGCTCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 426

GGCCGTGGCGCCGTTTTCAACGGAGTCCGGGGAGACCATTCGTGCCACGCTCTTTCCCGGCGATGGCATCGGGCCAGAGATCGCTGAGTCTGTCAAGCAGgtacagaatt ... gtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagaaggttgcttgtttctatgatgtcttaatatttttgttttgtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG
                           tcttaat  putative branch site (score: 426)
                             ttaatatttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctactgttgttaactagtgtatgaagttcattgatgcatgatatctgagaaggttgcttgtttctatgatgtcttaatatttttgttttgtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
gctactg
- - - - - - - - -gtgtatg
- - - - - - - - - - - - - - - - - -tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatgt