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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattacccacaactctcaacttttgatccatggtatctagagtttattggaatatgctatacgccaagcttttcttattgttgtaacttatgcttgattcataataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGATGAGGATGGTTGTTTCCGATATATTGGTGGCTATTGGGAAACAAGAGAAA

Basic information

species Glycine max
transcript GLYMA18G01590.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G156608_T03 (Zea mays), 3'ss of exon 2
gtaaattacccacaactctcaacttttgatccatggtatctagagtttattggaatatgctatacgccaagcttttctt-----attgttgtaacttatgcttgattcataataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGATGAGGATGGTTGTTTCCGATATATTGGTGGCTATTGGGAAACAAGAGAAA
                     | |  ||| | | | | |     |  ||||  |             ||   || | ||     || || ||   |||    | ||     |   | |||||| || |  ||||||||| |||||||  |||||| ||||||||||||||||| |  |   ||| ||| ||||| ||||| || |||||| | || || |
--------------------tagtggtgaacaaagatcttagttgggtattcaagctcatccctgagcagatttctttttgttcatcgtggtgctttacctctcatggtatactttgcagGCACGACAACTGCAAGAAAAAGGATGGAGACCAAGGTGGTTTAAGAAGGATGATGGCGACAGTTACCGCTATATGGGTGGATACTGGGAAGCGAGGGAGA
















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|193675874|gb|FK620028.1|FK620028
EST:     ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTG                         GCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGA
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGA
EST: gi|207840404|gb|GD812165.1|GD812165
EST:     ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTG                         GCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
EST: gi|193473724|gb|FK441485.1|FK441485
EST:     ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTG                         GCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
EST: gi|23729543|gb|BU762863.1|BU762863
EST:     ATGAGCTGGCAAATGCAGAAAAACTAAGACTTGAACAGTTGCAGAGACAG                         GCAAGAAAGATGCAAGAA
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAA
EST: gi|208106764|gb|GD902325.1|GD902325
EST:     ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTG                         GCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
EST: gi|209724148|gb|BW659682.1|BW659682
EST:     ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTG                         GCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
EST: gi|208232008|gb|GE032769.1|GE032769
EST:     ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTG                         GCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
EST: gi|58015839|gb|CX702581.1|CX702581
EST:     ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTG                         GCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
EST: gi|14205607|gb|BG839285.1|BG839285
EST:     ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTG                         GCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
EST: gi|19268832|gb|BM885088.1|BM885088
EST:     ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTG                         GCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
EST: gi|58016257|gb|CX702999.1|CX702999
EST:     ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTG                         GCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT
genomic: ATGAGCTGGCAAATGCAGAGAAACTAAGACTTGAACAGTTGCAGAGACTGgtaaattacc ... aataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacgccaagcttttcttattgttgtaacttatgcttgattcataataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGATGAGGATGGTTGTTTCCGATATATTGGTGGCTATTGGGAAACAAGAGAAA
                                    ttgattcataataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattacccacaactctcaacttttgatccatggtatctagagtttattggaatatgctatacgccaagcttttcttattgttgtaacttatgcttgattcataataattcagGCAAGAAAGATGCAAGAAAGAGGATGGCAACCAAGATGGTTTAAGAAGGATGAGGATGGTTGTTTCCGATATATTGGTGGCTATTGGGAAACAAGAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA