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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCTAGAAGCGGCGGCGGTGCCAGGGTTCGGCGCTCGGTCGGCAATGGCGAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgctagtggcttgttgttattgagaatgttacgatccttcagttgcgtgcttgttttagtgttgttagcaacgcgtggacggcgagatgccttg...

Basic information

species Zea mays
transcript GRMZM2G005082_T01
intron # 1
splice site 5'
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|60356073|gb|DN223046.1|DN223046
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|148958789|gb|EE010405.2|EE010405
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|21987505|gb|BQ779033.1|BQ779033
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|211085009|gb|FL055872.1|FL055872
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|149094664|gb|EE180208.2|EE180208
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|149105010|gb|EE290485.2|EE290485
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|71433997|gb|DR815047.1|DR815047
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|76917879|gb|DV167052.1|DV167052
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|89251281|gb|DY623067.1|DY623067
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|148960780|gb|EE011439.2|EE011439
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|148960186|gb|EE153438.2|EE153438
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|211085006|gb|FL055869.1|FL055869
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|26558271|gb|CA830506.1|CA830506
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|86465853|gb|DY232226.1|DY232226
EST:     GAGGCGGTTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAGTGCCACGGCGGCAAGATTGGTGTCTGCTACGGCCGCAACGCCGAAG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|148970144|gb|EE021085.2|EE021085
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
EST: gi|9825046|gb|BE575248.1|BE575248
EST:     GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCG                         GGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG
genomic: GAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACG

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), 46 (downstream exon)
Score: 653

GGGCTAGAAGCGGCGGCGGTGCCAGGGTTCGGCGCTCGGTCGGCAATGGCGAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACGACCTTCCGGCGCCAGACAAGGTGGCGCAGCTAATCCAGCAGCAGTCCAT


Block sizes: 49 (upstream exon), 31 (downstream exon)
Score: 29

GGGCTAGAAGCGGCGGCGGTGCCAGGGTTCGGCGCTCGGTCGGCAATGGCGAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACGACCTTCCGGCGCCAGACAAGGTGGCGCAGCTAATCCAGCAGCAGTCCAT


Block sizes: 32 (upstream exon), 31 (downstream exon)
Score: 8

GGGCTAGAAGCGGCGGCGGTGCCAGGGTTCGGCGCTCGGTCGGCAATGGCGAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACGACCTTCCGGCGCCAGACAAGGTGGCGCAGCTAATCCAGCAGCAGTCCAT


Block sizes: 46 (upstream exon), 31 (downstream exon)
Score: 29

GGGCTAGAAGCGGCGGCGGTGCCAGGGTTCGGCGCTCGGTCGGCAATGGCGAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgct ... gcaatcgcagGGCAATGCCACGGCGGCAAGATTGGCGTCTGCTACGGCCGCAACGCCGACGACCTTCCGGCGCCAGACAAGGTGGCGCAGCTAATCCAGCAGCAGTCCAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCTAGAAGCGGCGGCGGTGCCAGGGTTCGGCGCTCGGTCGGCAATGGCGAGGCGGCTTATGCTGGCGCTCCCTGTGCTCCTCTTCTTATTGCTCGTCGgtgagttgctagtggcttgttgttattgagaatgttacgatccttcagttgcgtgcttgttttagtgttgttagcaacgcgtggacggcgagatgccttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC