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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagaggaggaaaaacatagatgaataatgtatctttaatttttcctttgggtacaagattaattaatgtctgattttatgtgttggtgtgttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA

Basic information

species Glycine max
transcript GLYMA07G15170.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 1
taagaggaggaaaaacata-gatgaataatgtatctttaatttttcctttgggtacaagattaattaatgtctgattttatg-tgttggtgtgttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
| |      |      ||  |   | | ||  | ||  | | |  | ||| |   | |  |     |    ||| |    || |  || ||     |||||||| ||||| |||||| ||||||||||||| ||||||||||| || ||
tcaatttctgtgggcgatgcgcctactgattgagctgcagtat--cgttttgaccccatttcttgaagcaactgctcacctgctactgttgctgatctgcagACTTACCCGAATCCTCTGCAAGACAACCCGGCTTATTCAGTCGTCAA

upper sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G080375_T03 (Zea mays), 3'ss of exon 1
-taagaggaggaaaaacatagatgaataatgtatctttaatttttcctttgggtacaagattaattaatgtctgattt-tatgtgttggtgtgttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
  |   |||| |  | |||    ||  || | |     |          ||     ||  ||  || |||| | | |  |   || ||  ||    |||||||||||||| |||||| | ||||||||||| || |||||||| || ||
tcagagggagaatcagcatccgagagaaaggcaaac--agcaaaaaacatgatatgaacttttttttatgtttcactgatcactgatgtcgtcgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
















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|208332905|gb|GE131466.1|GE131466
EST:     ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCA                         ACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
genomic: ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCAgtacgtcgtc ... gttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
EST: gi|213598739|gb|DB956636.1|DB956636
EST:     ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCA                         ACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
genomic: ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCAgtacgtcgtc ... gttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
EST: gi|17023871|gb|BM094905.1|BM094905
EST:     ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCA                         ACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
genomic: ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCAgtacgtcgtc ... gttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
EST: gi|151398093|gb|EV267971.1|EV267971
EST:     ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCA                         ACATACCCTAATCCTTTGCAAGACGACCCTGCTTATTCAGTTGTTAA
genomic: ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCAgtacgtcgtc ... gttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
EST: gi|151396687|gb|EV266560.1|EV266560
EST:     ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCA                         ACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
genomic: ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCAgtacgtcgtc ... gttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
EST: gi|209711853|gb|BW674115.1|BW674115
EST:     ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCA                         ACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
genomic: ACATCCTCGAAGACGTTCCGCATTTCACCGATTACATTCCCAATCTCCCAgtacgtcgtc ... gttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgggtacaagattaattaatgtctgattttatgtgttggtgtgttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA
             attaattaatgtctga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagaggaggaaaaacatagatgaataatgtatctttaatttttcctttgggtacaagattaattaatgtctgattttatgtgttggtgtgttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA