Sequence
atgc intronic sequence ATGC exonic sequencegtatttatttgttttgacactctatatttcatttttaatcttccttctgtaactgtattttggaaatggaagactttcttatccattgctgctttcttttaatgtaattgtacagCCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGGCCAACTGGAGTTTATCCTCAATACTATGCAGCAT
Basic information
species | Glycine max |
transcript | GLYMA04G42250.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G42250.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G21380.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatttatttgttttgacactctatatttcatttttaatcttccttctgtaactgtattttggaaatggaagactttcttatccattgctgctt--tct-----tttaatgtaattgtacagCCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGGCCAACTGGAGTTTATCCTCAATACTATGCAGCAT
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------------------------------gtttttgtttaccattctcttacctgcttgttatatttcaa--ttctgttatccaat-ctgcttaacctggaaatttatcaaatttatacagCCAGACCTGACTGTGAGGGAGAAGATACTTAGTTTATTAGATACATGGCAAGAAGCTTTTGGTGGAAGCGGCGGAAGATTCCCTCAGTACTACAATGCCT
upper sequence: GLYMA04G42250.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G76970.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatttatttgttttgacactctat-atttcatttttaatcttccttctgtaactgtattttggaaatggaagactttcttatccattgctgctttcttttaatgtaattgtacagCCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGGCCAACTGGAGTTTATCCTCAATACTATGCAGCAT
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----------gttttgctataatttcacctcacctgcctctaatatctcgaatttctatatttgatattgtat-ctctcttacc--ttgtaaatttcct--aacataatttggcagCCGGAACTGAATGTGAGGGAAAAGATACTAACTTTGTTAGACACATGGCAAGAAGCCTTTGGTGGACGTGGAGGTCGATACCCACAATACTACAATGCCT
upper sequence: GLYMA04G42250.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g01180.t01 (Vitis vinifera), 3'ss of exon 3
gtatttatttgttttgacactctatatttcatttt---taatcttccttctgtaactgtattttggaaatggaagactttcttatc-catt-gctgctttcttttaatgt--aattgtacagCCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGGCCAACTGGAGTTTATCCTCAATACTATGCAGCAT
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------------------gtgcctaatttcatcctggcttgttttatgtatatatatatatatcatggcttgttgttttcattctcatattagtttatttttatctatgttcaaatctgcagCCAGACTTGAATGTAAGGGAAAAGATTCTAATTTTGATAGATACGTGGCAAGAAGCTTTTGGGGGACCTAGGGGAAGATATCCCCAATACTATGCTGCATMapped 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|208264627|gb|GE063947.1|GE063947EST: TCATTGAGCGGGATATCTTACATGAAATGGTTAAGATAGTGAAGAAGAAG CCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAA
genomic: TCATTGAGCGGGATATCTTACATGAAATGGTTAAGATAGTGAAGAAGAAGgtatttattt ... aattgtacagCCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAA
EST:
gi|207848805|gb|GD818836.1|GD818836EST: NCATTGAGCGGGATATCTTACATGAAATGGTTAAGATAGTGAAGAAGAAG CCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAA
genomic: TCATTGAGCGGGATATCTTACATGAAATGGTTAAGATAGTGAAGAAGAAGgtatttattt ... aattgtacagCCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaaatggaagactttcttatccattgctgctttcttttaatgtaattgtacagCCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGGCCAACTGGAGTTTATCCTCAATACTATGCAGCAT
ttttaat putative branch site (score: 3)
tttcttttaatgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttatttgttttgacactctatatttcatttttaatcttccttctgtaactgtattttggaaatggaagactttcttatccattgctgctttcttttaatgtaattgtacagCCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGGCCAACTGGAGTTTATCCTCAATACTATGCAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC