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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacttggtttttctgtacctaccctctatttttgtttgtgttttacctccacttatgctctccctgtttggctgataatgaaatatattgtttttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG

Basic information

species Glycine max
transcript GLYMA04G01100.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
gttacttggtttttctgtacctaccctctatttttgtttgtgttttacctccacttatgctctccctgtttggctgataatgaaatatattgtt------tttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG
                            | ||||| ||    ||||  ||    | | | | |   |  |    ||||  || | |   | |||      ||||||||||| ||||| |||||||| |||||||||||||||||||| || || || || || |||||||||||||
--------------------------gttgtttttcttaagcttttgactagtttgaagttttgattact--attgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG

upper sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 2
gttacttggtttttctgtacctaccctctattt-ttgtttgtgttttacctccacttatgctctccctgtttggctgataatgaaatatattgtttttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG
                     ||| |  |   | ||  || | | | ||   |   |||    |  ||  ||  |   |    |    | |   |    ||||||  |||||||||||||||||||||||||||||||  || || ||||| |||||||||||||||||||
-------------------gttacacaatgcctcttacttctatgtaactgtcctgtata---tttcttcttaacctttgtatatccttttctctcactagCATTTCCAAAGGGATATTGTCCGTGGTGTGGAAGGTTTCATAGTTACTGGGTCCAAGCAAGTTGAAATAG

upper sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 2
gttacttggtttttctgtacctaccctctatttttgtttgtgttttacctccacttatgctctccctgtttggctgataatgaaatatattgtttttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG
||| |||  |  | ||||   |    | |   |   ||||| | || |||| ||||||    | |                    |||||  |||||||||||| ||||||||||||||| |||||||| ||||||| ||| || ||||| ||||| |||||||||||||
gttgcttaatcctcctgtggttcatttgtgactcaatttgtttatttcctcaacttataaatttc--------------------tatatcatttttcagCATTTTCAAAGGGATATTGTTCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAG

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|24136864|gb|BU927374.1|BU927374
EST:     AGCAACATCAGAAACTTGAGAAGCTTTACATATCAACACGTGCTGGAAAG                         CATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGA
genomic: AGCAACATCAGAAACTTGAGAAGCTTTACATATCAACACGTGCTGGAAAGgttacttggt ... tgtttttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGA
EST: gi|18039567|gb|BM307861.1|BM307861
EST:     AGCAACATCAGAAACTTGAGAAGCTTTACATATCAACACGTGCTGGAAAG                         CATTATCAAAGGGATATTGTCCGCGGTGTGGAAGGTTATATTGTAACTGGA
genomic: AGCAACATCAGAAACTTGAGAAGCTTTACATATCAACACGTGCTGGAAAGgttacttggt ... tgtttttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGA
EST: gi|298187568|gb|HO034717.1|HO034717
EST:     AGCAACATCAGAAACTTGAGAAGCTTTACATATCAACACGTGCTGGAAAG                         CATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGA
genomic: AGCAACATCAGAAACTTGAGAAGCTTTACATATCAACACGTGCTGGAAAGgttacttggt ... tgtttttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGA
EST: gi|5126412|gb|AI748148.1|AI748148
EST:     AGCAACATCAGAAACTTGAGAAGCTTTACATATCAACACGTGCTGGAAAG                         CATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGA
genomic: AGCAACATCAGAAACTTGAGAAGCTTTACATATCAACACGTGCTGGAAAGgttacttggt ... tgtttttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGA
EST: gi|16347039|gb|BI972634.1|BI972634
EST:     AGCAACATCAGAAACTTGAGAAGCTTTACATATCAACACGTGCTGGAAAG                         CATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGA
genomic: AGCAACATCAGAAACTTGAGAAGCTTTACATATCAACACGTGCTGGAAAGgttacttggt ... tgtttttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctccacttatgctctccctgtttggctgataatgaaatatattgtttttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG
                          ggctgat  putative branch site (score: 4)
                                            ttgtttttc  putative PPT
                             tgataatgaaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacttggtttttctgtacctaccctctatttttgtttgtgttttacctccacttatgctctccctgtttggctgataatgaaatatattgtttttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG