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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttcacagttgctgtgtgacattgtaaatttcagcaccaatcctctgtagccaaaccctaacaaatcacgccttattcag

Basic information

species Zea mays
transcript GRMZM2G149952_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149952_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g53230.1 (Oryza sativa), 5'ss of exon 4
GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagt----tttcacagttgctgtgtgacattg--taaatttcagcaccaat---cctctgtagccaaaccctaacaa-atcac--gccttattcag
|||||||| |||||||||||||||||||||||||| || || |||||||||||||||||||||||||||||||||||||||||||||||||      |||||    || | ||  |||     ||| ||| |||||||||     | |  |||| |  |||||||| ||  |  |  ||||  ||
GTGGCTGCATATGACACAAAGCAAAAGAAAATGGACTTTTTCGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaacatccatttcaatcctgttttggtacaccagttaattttgagcaccaatgtttttttccagcccagtcctaacaacattgcctgtgttatatag
















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|32920504|gb|CF025316.1|CF025316
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|32829670|gb|CD969348.1|CD969348
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGTGAGAGTCCCCCAGATGGTTTTATG
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATG
EST: gi|32830909|gb|CD970587.1|CD970587
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGTGAGAGTCCCCCAGATGGTTTTATG
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATG
EST: gi|37387177|gb|CF630781.1|CF630781
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|149040632|gb|EE046873.2|EE046873
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATTTTTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|32831393|gb|CD971071.1|CD971071
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGTGAGAGTCCCCCAGATGGTTTTATG
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATG
EST: gi|211229396|gb|FL476090.1|FL476090
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|32831832|gb|CD971510.1|CD971510
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGTGAGAGTCCCCCAGATGGTTTTATG
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATG
EST: gi|16926603|gb|BM079671.1|BM079671
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|76287850|gb|DV027418.1|DV027418
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|60342436|gb|DN209409.1|DN209409
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|37390063|gb|CF632257.1|CF632257
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|32829476|gb|CD969154.1|CD969154
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGTGAGAGTCCCC-AGATGGTTTTATG
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATG
EST: gi|60345908|gb|DN212881.1|DN212881
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|32829296|gb|CD968974.1|CD968974
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGTGAGAGTCCCC-AGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|40336006|gb|CK370076.1|CK370076
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|60357535|gb|DN224508.1|DN224508
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGC
EST: gi|32831003|gb|CD970681.1|CD970681
EST:     TCTTTGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGTGAGAGTCCCCCAGATGGTTTTATG
genomic: TCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATG

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: 46 (upstream exon), 29 (downstream exon)
Score: 24

GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGCCCGGGTGGCTGGAAGGTACTCGTTGAATACTATGACAGCTTGGTGCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 782

GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGCCCGGGTGGCTGGAAGGTACTCGTTGAATACTATGACAGCTTGGTGCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 705

GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGCCCGGGTGGCTGGAAGGTACTCGTTGAATACTATGACAGCTTGGTGCCAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 75

GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGAGAGAGTCCCCCAGATGGTTTTATGTGCCCGGGTGGCTGGAAGGTACTCGTTGAATACTATGACAGCTTGGTGCCAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCTGCGTATGACACAAAGCAAAAGAAAATGGATTTCTTTGATCCATCAAGGAAAGATGATTTCCTGTTCATCTCTGGCACAAAGgtaagttttcacagttgctgtgtgacattgtaaatttcagcaccaatcctctgtagccaaaccctaacaaatcacgccttattcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG