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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcaaaacttgaagccttggcaaatgtggccactttgtatgagcgatgtgattcttttcgtaaacttgaagcattgacaaatgtggctttacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAGCTGCCACTGGTGCCATTACCTGAACTGCGTACCAACGTCCAGATGGAAG

Basic information

species Zea mays
transcript GRMZM2G157384_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157384_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g43320.1 (Oryza sativa), 3'ss of exon 4
------aatcaaaacttgaagccttggcaaatgtggccactttgta--tgagcgatgtgattcttttcgtaaacttgaagcattgacaaatgtggctttacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAGCTGCCACTGGTGCCATTACCTGAACTGCGTACCAACGTCCAGATGGAAG
       |   | |    |   ||||   || |   |   ||   |  | | | ||  ||  || |      || |||| |  ||||| | |||  ||   | ||||||||||  |||  | |||| ||||| |||| ||| |||||||| |||||  | || ||||||||||| |||||||||||| ||||||| ||||||||||||
gctatagactgacataaaatagcttgaataa-gcaacagtttgacaattcatcaataagaagctat------acctgaaac-ctgacagaggtgaattactgatgcagGTTTGTGATTGCCCTGGTGATGCTTTTCAAGGGGAAGAATGGAAACGATGGTTGTCACTGGTGCCACTACCTGAACTGCATACCAACATCCAGATGGAAG
















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|60342822|gb|DN209795.1|DN209795
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|78088538|gb|DV516931.1|DV516931
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|40335119|gb|CK369189.1|CK369189
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|88752104|gb|DY536245.1|DY536245
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|7216855|gb|AW562977.1|AW562977
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCAAGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|211377148|gb|FL183044.1|FL183044
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAAT-GTAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|211377150|gb|FL183046.1|FL183046
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAAT-GTAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|5499565|gb|AI855432.1|AI855432
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|22521141|gb|BU079952.1|BU079952
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCAAGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|148941580|gb|EC886517.2|EC886517
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|71762229|gb|DR960166.1|DR960166
EST:     TCGTACCAGTATGTTTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|87156908|gb|DY401697.1|DY401697
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCAAGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|74236231|gb|DT644145.1|DT644145
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|86468306|gb|DY234676.1|DY234676
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|76289251|gb|DV028819.1|DV028819
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|26559005|gb|CA831240.1|CA831240
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCAAGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|211377149|gb|FL183045.1|FL183045
EST:     CCAGTATG--TTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: CCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|211198133|gb|FL454862.1|FL454862
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|74241937|gb|DT649851.1|DT649851
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGAAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|37380344|gb|CF626976.1|CF626976
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
EST: gi|78023347|gb|DV491734.1|DV491734
EST:     TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGG                         GTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG
genomic: TCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAG

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: 79

GGATGGAACGCAGCGAGCTACCTCAGACTAGTCAACCTCCAAAGTACAAATCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAGCTGCCACTGGTGCCATTACCTGAACTGCGTACCAACGTCCAGATGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GGATGGAACGCAGCGAGCTACCTCAGACTAGTCAACCTCCAAAGTACAAATCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAGCTGCCACTGGTGCCATTACCTGAACTGCGTACCAACGTCCAGATGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 107

GGATGGAACGCAGCGAGCTACCTCAGACTAGTCAACCTCCAAAGTACAAATCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAGCTGCCACTGGTGCCATTACCTGAACTGCGTACCAACGTCCAGATGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

GGATGGAACGCAGCGAGCTACCTCAGACTAGTCAACCTCCAAAGTACAAATCGTACCAGTATGTCTTGTGGGTTGCTGCACTCCTCTTGCTGGTAGTTGGgtaagtttca ... tacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAGCTGCCACTGGTGCCATTACCTGAACTGCGTACCAACGTCCAGATGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtgattcttttcgtaaacttgaagcattgacaaatgtggctttacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAGCTGCCACTGGTGCCATTACCTGAACTGCGTACCAACGTCCAGATGGAAG
                           cattgac  putative branch site (score: 114)
      attctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcaaaacttgaagccttggcaaatgtggccactttgtatgagcgatgtgattcttttcgtaaacttgaagcattgacaaatgtggctttacgttgcagGTTTGCCATTATCTTGGTCATGCTCTTCACGGGTAAGAATGGGAACGACAGCTGCCACTGGTGCCATTACCTGAACTGCGTACCAACGTCCAGATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
aatcaaa
- - - - - - - - - - gcaaatg
- - - - - - - - - - - - - - - - - -ttgtatg
- - - - - - - - - - - - - - - - - - - - - - cgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggct