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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcatgctttgttttctctaggatttacaaccactgaagataaagcactgaattttattgtttcactaatttgggttcctgttctttggatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGAAGAAAGGTCGGGGAAGGAGACAATGATGCCGGTCTGGTTCTTATTTCTT

Basic information

species Zea mays
transcript GRMZM2G058407_T01
intron # 3
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|44682050|gb|CK787098.1|CK787098
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186460|gb|FL239191.1|FL239191
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|32863264|gb|CF002946.1|CF002946
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|76292025|gb|DV031593.1|DV031593
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211188850|gb|FL239192.1|FL239192
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|32936820|gb|CF041639.1|CF041639
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCAAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186450|gb|FL239181.1|FL239181
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|45213689|gb|CK849962.1|CK849962
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGGTG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186452|gb|FL239183.1|FL239183
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|32937577|gb|CF042396.1|CF042396
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCAAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186458|gb|FL239189.1|FL239189
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186455|gb|FL239186.1|FL239186
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|32864829|gb|CF004511.1|CF004511
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|116818620|gb|EC861668.1|EC861668
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186449|gb|FL239180.1|FL239180
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|32936664|gb|CF041483.1|CF041483
EST:     GGAGAAGCTCACCAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCAAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|32906973|gb|CF011786.1|CF011786
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACGGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186448|gb|FL239179.1|FL239179
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186459|gb|FL239190.1|FL239190
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186451|gb|FL239182.1|FL239182
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186454|gb|FL239185.1|FL239185
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGC
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGC
EST: gi|44681672|gb|CK786720.1|CK786720
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|33942654|gb|CF349254.1|CF349254
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186453|gb|FL239184.1|FL239184
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211089528|gb|FL476391.1|FL476391
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTYTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186456|gb|FL239187.1|FL239187
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|211186447|gb|FL239178.1|FL239178
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
EST: gi|76292026|gb|DV031594.1|DV031594
EST:     GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG                         CTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA
genomic: GGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGA

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: 24

TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGAAGAAAGGTCGGGGAAGGAGACAATGATGCCGGTCTGGTTCTTATTTCTT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 34

TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGAAGAAAGGTCGGGGAAGGAGACAATGATGCCGGTCTGGTTCTTATTTCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 55

TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGAAGAAAGGTCGGGGAAGGAGACAATGATGCCGGTCTGGTTCTTATTTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATGgtatcatgct ... gatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGAAGAAAGGTCGGGGAAGGAGACAATGATGCCGGTCTGGTTCTTATTTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcactgaattttattgtttcactaatttgggttcctgttctttggatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGAAGAAAGGTCGGGGAAGGAGACAATGATGCCGGTCTGGTTCTTATTTCTT
                    cactaat  putative branch site (score: 108)
       aattttattgtttcac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcatgctttgttttctctaggatttacaaccactgaagataaagcactgaattttattgtttcactaatttgggttcctgttctttggatcgtgcagCTGATATCAGTGAAGTTTCAGAGAAGGGACAGGCCGAGCAACAGCAACCGAAGAAAGGTCGGGGAAGGAGACAATGATGCCGGTCTGGTTCTTATTTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA