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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggttctgatctgataacaagtttacgcccttttcggctttgctgttcatgtgcgcctgttgttgatgatcacgtgccttgtgctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC

Basic information

species Zea mays
transcript GRMZM2G174204_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 2
gtgcggttctgatctgataacaagtttacgcccttttcggctttgctgttcatgtgcgcctgttgttgatgatcacgtgccttgtgctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC
||| |   ||| |   ||  |       |  | | |      ||  | ||  || |   |||||| |||||  | || |  |||| |||  ||||||| ||||||||||||| ||||||||||||||||| || ||||| |||||||| ||||||||||||||
gtgagagactgtttatattccccccccccctcttctgttcaattttttttggtgcgtttctgttgctgatgcgcgcgcgt-ttgttctgtggcagTTGCTTGGTGCTAAGGGTAAGAGGTTCGCCAAGAAGCGGTATGCCGAGAAGGCACAGATGAAGAAGAC

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 2
gtgcggttctgatctga-taacaagttt--acgcccttttcggctttgctgttcatgtgcgcctgttgttgatgatcacgtgcc--ttgtgctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC
     |||   |||  | |   || |||  |     ||||   | | | | |           | |  ||  ||      ||    ||    ||    ||    | |||  ||||||||| | | | |||||||||   |||||||| ||||||||||||||||||||
-----gtttaaatcaaaattttaaattttaattgtttttttaacatagttttattgcaataattctaattattggatttttgttaatttgaatggaatagGCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 2
gtgcggttctgatctgataacaagtttacgcccttttcggct-----ttgctgttcatgtgcgcctgttgt-tgatgatcacgtgccttgtgctgctgcagTTGATTG-------------GTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC
|| |  || | || |||||    |||| |  |    |||  |     |   | ||| |      ||||  | |||| ||  | ||  ||       || | |||||||             ||  |||||| |||| ||| || |||||||| ||||| || ||||||||||||||||| ||
gt-ctttttttatttgatattctgttttcttctcagtcgattaattctatgttttcttagttttctgtaatgtgataatttcatgtttttctggtttgaatttgattgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAGGCGCAGATGAAGAAAAC

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|78109120|gb|DV527537.1|DV527537
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|37398604|gb|CF636617.1|CF636617
EST:     -AGCCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAA-GACGCCCCGCAAT                         TTGATT-GTGCTAGGGGC-AGAGGTTTCGCCAAGAAACGCTATGCTGAGA
genomic: AAG-CGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACG-CCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGG-TTCGCCAAGAAACGCTATGCTGAGA
EST: gi|211464729|gb|FL207495.1|FL207495
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211464737|gb|FL207503.1|FL207503
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211464734|gb|FL207500.1|FL207500
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|14883663|gb|BI273476.1|BI273476
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|149079698|gb|EE168699.2|EE168699
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211464740|gb|FL207506.1|FL207506
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|15053622|gb|BI359167.1|BI359167
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211464732|gb|FL207498.1|FL207498
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211467266|gb|FL207509.1|FL207509
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|71440546|gb|DR821596.1|DR821596
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|148933462|gb|EC877158.2|EC877158
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|15053623|gb|BI359168.1|BI359168
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|50332541|gb|CO527667.1|CO527667
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|22545768|gb|BU098142.1|BU098142
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|31359359|gb|CD443716.1|CD443716
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGGTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211462211|gb|FL207488.1|FL207488
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211464730|gb|FL207496.1|FL207496
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|15313826|gb|BI478973.1|BI478973
EST:     GCANGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|211462214|gb|FL207491.1|FL207491
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|76917038|gb|DV166648.1|DV166648
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
EST: gi|22819549|gb|BU499639.1|BU499639
EST:     GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAAT                         TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG
genomic: GCAAGCGCGAGGCGCGCGAGGTGCACAGGCGCTCGAAGGACGCCCGCAATgtgcggttct ... gctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgctgttcatgtgcgcctgttgttgatgatcacgtgccttgtgctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC
                       tgttgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcggttctgatctgataacaagtttacgcccttttcggctttgctgttcatgtgcgcctgttgttgatgatcacgtgccttgtgctgctgcagTTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG