Sequence
atgc intronic sequence ATGC exonic sequencegtatgttttatatgaaattttaattcttgccttgttaattatgttatggttaccaacttatttactcagtgacgtatttgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTTGATGCCAAAACTGCAAAAGCGTTCAAAGAGAAGATTGATGATGAGTATC
Basic information
species | Glycine max |
transcript | GLYMA14G11780.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G11780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G25100.2 (Arabidopsis thaliana), 3'ss of exon 3
gtatgttttatatgaaattttaattcttgccttgttaattatgttatggttaccaacttatttactcagtgacgtatttgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTTGATGCCAAAACTGCAAAAGCGTTCAAAGAGAAGATTGATGATGAGTATC
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-----gtttgtctctgttttgatacatttatgtatttctctttacttgactgctaacttgtggagtttggaataa---tgtagTTTAAAATGCGTGAGGCGCAAATGTGTAATGTTCTCGGTCGTGTTATGCTTGATGCAAAGTCTGCCAAAGCGTTTAAAGAGAAGATTGATGATGAGTATC
upper sequence: GLYMA14G11780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 2
---------gtatgttttatatgaaattttaattc-ttgccttgttaattatgttatggttaccaacttattt--actc-------agtgacgtatttgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTTGATGCCAAAACTGCAAAAGCGTTCAAAGAGAAGATTGATGATGAGTATC
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gttagtctcgtattcaatttttaattttgtaattcatcaggctgtcaaaaatattatgtctgtgatttaactctaacccttgcggggctgaaacaattgcagTTTAAAATGCGGGAGGCACAAATGTGCAATATTCTCGGCCGGGTCACTCTTGATGCCAAGACAGCTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACC
upper sequence: GLYMA14G11780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g06640.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtttta----tatgaaattttaa----ttcttgccttgttaattatgttatggttaccaacttattta-ctcagtgacgtatttgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTTGATGCCAAAACTGCAAAAGCGTTCAAAGAGAAGATTGATGATGAGTATC
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gtcagttttaacatcttgcttttttgacaagttgagggctgcttgtttatgtta--ataattgactcttttagctgagtggatttgttgcagTTTAAAATGCGGGAACCACAGTTGTGCAATGTTATCTGCCACCTAAAACTCAATGCAAAAACTGCGAAGGATTTTAAAGAGAAGATTGAAGATGAGTATCMapped 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|209716722|gb|BW654317.1|BW654317EST: ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTG TTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
genomic: ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgtttta ... gtatttgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
EST:
gi|209711818|gb|BW674078.1|BW674078EST: ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTG TTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
genomic: ATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgtttta ... gtatttgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccttgttaattatgttatggttaccaacttatttactcagtgacgtatttgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTTGATGCCAAAACTGCAAAAGCGTTCAAAGAGAAGATTGATGATGAGTATC
tgttaat putative branch site (score: 3)
ttaattatgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttttatatgaaattttaattcttgccttgttaattatgttatggttaccaacttatttactcagtgacgtatttgcagTTTAAAATGCGTGAACCACAAATGTGCAATATTGTGTGTAAGCTTAAACTTGATGCCAAAACTGCAAAAGCGTTCAAAGAGAAGATTGATGATGAGTATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA