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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcctctattttactcctgaaacttccttgttttcacattcttttgaaactgaagttaatttgactgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAGGGGACTACTCTTAAG

Basic information

species Glycine max
transcript GLYMA02G01930.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 15
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 16
---------------------------gtaagtttcctctattttactcctgaaacttcct-tgttttcacattcttttgaaact---gaagttaatttgactgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAGGGGACTACTCTTAAG
                            |     || ||  ||||||   |   | | |   ||  |  || ||  |    |  |   |||      |   || | |||||||||||| |||||||| || ||| |||||||||||| |||||||||||| ||   |||  | |||
gtaagtctctaaatattgaactccgcctttttagtcatccgttttaccattaggattactaatgaatgtactttgatgctgagttttggaatccttatcctctttaccagAAAATCGGGTATGACAATGCTGCAGCAGTTGCCAAGAAAGCTCACAAAGAAGGATGTACATTGAAG

upper sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S49_154V6.1 (Physcomitrella patens), 3'ss of exon 15
---------------------------------------------------------------------------------------gtaagtttcctctattt-tactcctgaaacttccttgttttcacattcttttgaaactgaa--gttaatttgactgttc-----cagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAGGGGACTACTCTTAAG
                                                                                           |||  ||  ||   |||   ||     |   |||   ||   |||   |||   | |  | | |||| | | ||      |||||||| ||||||||||| || ||| ||  ||| |||| |||||||||||| ||||||||  | |||
gtaagttcacttgccttctttttgtgcgtttaattaagttggacggctgctattattttgaaaggagattttattgctctatgcgtttggggttgtcttgatgagtacaattgtgtgctgagtgtggacattctctccggaagtggcattgctgatttcattcttgttgggcagAAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAG
















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|51344356|gb|CO985089.1|CO985089
EST:     TCACTTATGCTTGTCACATCCTTAAACCCA                         AAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
genomic: TCACTTATGCTTGTCACATCCTTAAACCCAgtaagtttcc ... actgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
EST: gi|31561807|gb|CD487645.1|CD487645
EST:     TCACTTATGCTTGTCACATCCTTAAACCCA                         AAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
genomic: TCACTTATGCTTGTCACATCCTTAAACCCAgtaagtttcc ... actgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
EST: gi|26047345|gb|CA784166.1|CA784166
EST:     TCACTTATGCTTGTCACATCCTTAAACCCA                         AAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
genomic: TCACTTATGCTTGTCACATCCTTAAACCCAgtaagtttcc ... actgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
EST: gi|31458946|gb|CD400974.1|CD400974
EST:     TCACTTATGCTTGTCACATCCTTAAACCCA                         AAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
genomic: TCACTTATGCTTGTCACATCCTTAAACCCAgtaagtttcc ... actgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
EST: gi|192307576|gb|FG999615.1|FG999615
EST:     TCACTTATGCTTGTCACATCCTTAAACCCA                         AAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
genomic: TCACTTATGCTTGTCACATCCTTAAACCCAgtaagtttcc ... actgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
EST: gi|51336381|gb|CO980247.1|CO980247
EST:     TCACTTATGCTTGTCACATCCTTAAACCCA                         AAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
genomic: TCACTTATGCTTGTCACATCCTTAAACCCAgtaagtttcc ... actgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
EST: gi|13252662|gb|BG363565.1|BG363565
EST:     TCACTTATGCTTGTCACATCCTTAAACCCA                         AAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
genomic: TCACTTATGCTTGTCACATCCTTAAACCCAgtaagtttcc ... actgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
EST: gi|10237782|gb|BE806670.1|BE806670
EST:     TCACTTATGCTTGTCACATCCTTAAACCCA                         AAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
genomic: TCACTTATGCTTGTCACATCCTTAAACCCAgtaagtttcc ... actgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
EST: gi|51343889|gb|CO984622.1|CO984622
EST:     TCACTTATGCTTGTCACATCCTTAAACCCA                         AAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
genomic: TCACTTATGCTTGTCACATCCTTAAACCCAgtaagtttcc ... actgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
EST: gi|7640202|gb|AW734508.1|AW734508
EST:     TCACTTATGCTTGTCACATCCTTAAACCCA                         AAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG
genomic: TCACTTATGCTTGTCACATCCTTAAACCCAgtaagtttcc ... actgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacttccttgttttcacattcttttgaaactgaagttaatttgactgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAGGGGACTACTCTTAAG
                                        atttgac  putative branch site (score: 4)
                                              ctgttcc  CT-rich tract
                                  aagttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcctctattttactcctgaaacttccttgttttcacattcttttgaaactgaagttaatttgactgttccagAAAATCGGTTATGACAAGGCAGCAACAGTTGCCAAGACAGCTCACAAAGAGGGGACTACTCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG