Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatgtattgtatgtatttcccttttccctattgtctatctttttcctcgctaatgcattgcattgcagGACATCACGGCAGAAACAAATTGACTATGATGGTCATTCCAAGCATTTTTCTACCCGAAGACTGGTCATTCACTTTTTACGAAGGGATTAATAGACATCC
Basic information
species | Glycine max |
transcript | GLYMA12G28490.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------gtatgtatg---tattgtatgtatttcccttttccctattgtctatctttttcctcgcta-atgcattgcattgcagGACATCACGGCAGAAACAAATTGACTATGATGGTCATTCCAAGCATTTTTCTACCCGAAGACTGGTCATTCACTTTTTACGAAGGGATTAATAGACATCC
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tatatctctaacatcccattgctgcagatattggctaccttatgttcaggaaaccattcttgtatcagacaccaacatatctttatatttttttctatagGCTTTCAGTCCAGGAAAAAGTTAACCATGATGGTCATTCCTAGTATTTTTATTCCAGAAGACTGGTCATTTACATTTTATGAAGGACTTAACAGACATCC
upper sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 2
--------------------gtatgtatgtattgt--atgtatttcccttttccctattgt---ctatctttttcctcgctaatgcattgcat--tgcagGACATCACGGCAGAAACAAATTGACTATGATGGTCATTCCAAGCATTTTTCTACCCGAAGACTGGTCATTCACTTTTTACGAAGGGATTAATAGACATCC
| || | ||| |||| || | || | | | || || ||| | || | || ||| |||||| | ||| || || |||||||| |||||||| || || ||||||||| | || ||||||||||| || |||||||| ||||| | || ||||||||
ttttatttctgttttatctgatgattaaggattactgatgtggttgtttattgtccgatttgaattaactgttttgacacttctcttttacatgctgcagGCTACTGCGGGAGGAAGAAATTGACAATGATGGTGATCCCTAGCATTTTTATCCCAGAAGACTGGTCCTTTACTTTTTATGAAGGTCTGAACAGACATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttcccttttccctattgtctatctttttcctcgctaatgcattgcattgcagGACATCACGGCAGAAACAAATTGACTATGATGGTCATTCCAAGCATTTTTCTACCCGAAGACTGGTCATTCACTTTTTACGAAGGGATTAATAGACATCC
cgctaat putative branch site (score: 3)
tatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatgtattgtatgtatttcccttttccctattgtctatctttttcctcgctaatgcattgcattgcagGACATCACGGCAGAAACAAATTGACTATGATGGTCATTCCAAGCATTTTTCTACCCGAAGACTGGTCATTCACTTTTTACGAAGGGATTAATAGACATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA