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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgcatgcatcctcttcatggtgctatgttagcatagtgtactattatcagcttgtgcccattctacgtcaaaaatgtgtacacagttccaaat...

Basic information

species Zea mays
transcript GRMZM2G063909_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 6
GTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgcatgcatcctcttcatggtgctatgttagcatagtgtactattatcagcttgtgcccattctacgtcaaaaatgtgtacacagt-tccaaat
||||||||||| ||||||||||| | ||||||||||||||| |||||  |  | ||||| || ||||||  | || |  |         | | | | ||  | ||||| | ||  |  |        |      |||| ||  |   ||       | | | |||| 
GTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgtaaactataatgctacgataccataatggcataatatagaagcaaatttggatattttgtctatgtatatcttgaaattggaatgtgcaaa-

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 5
GTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgcatgcatcctcttcatggtgctatgttagcatagtgtactattatcagcttgtgcccattctacgtcaaa-----aatgtgtacacagttccaaat
|||||||| || |||||||| || ||||||||||||||||| |||||  |  | ||||| |||||||||  | || |      || |  ||||| ||||| || |||| | ||  |  |  ||    |      ||||  |  |      |||||| |     |   ||||
GTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGAGGAGgtatacttgtaa-----ctatgtatggttctatgataccataatataaaagcagaagtgcttattttgtctatatatatcttgtaatgtgcaatagatgaaaaat

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 6
GTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgta-------atcctgcatgcatcctcttcatggtgctatgttagcatag-tgtactat-tatcagcttgtgcccattc-tacgtcaaaaatgtgtacacagtt-ccaaat-----------
||  ||||||||||||||||||| | |||| |||||||||| || ||  |  | ||||| || ||||||       |  ||   |  ||  |    || |     |   | | ||| | ||  || |||||  |  | | | ||| |     ||   |||  |  || ||  |  ||           
GTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAGgtactgtataactctctgtatatagttacaatagcttggttagatcctagatatagaatatatcaaatgctcctccttcctgttctaaggctgttgatgcaattatcttatcattatttcag

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|71303469|gb|DR787844.1|DR787844
EST:     GAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCA
genomic: GAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCA
EST: gi|4609695|gb|AI600534.1|AI600534
EST:     GAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGT
genomic: GAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGT
EST: gi|211161741|gb|FL193319.1|FL193319
EST:     GAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCA
genomic: GAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCA
EST: gi|50331233|gb|CO526359.1|CO526359
EST:     GAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCA
genomic: GAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCA

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: 122

GTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCAACAGCAGTTGAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTCTGGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

GTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCAACAGCAGTTGAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTCTGGCTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 11

GTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCAACAGCAGTTGAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTCTGGCTTC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 59

GTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAGTGCCGAAAAGTGCTGCCAACAGCAGTTGAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTCTGGCTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgcatgcatcctcttcatggtgctatgttagcatagtgtactattatcagcttgtgcccattctacgtcaaaaatgtgtacacagttccaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG