Sequence
atgc intronic sequence ATGC exonic sequence...tatatctctaacatcccattgctgcagatattggctaccttatgttcaggaaaccattcttgtatcagacaccaacatatctttatatttttttctatagGCTTTCAGTCCAGGAAAAAGTTAACCATGATGGTCATTCCTAGTATTTTTATTCCAGAAGACTGGTCATTTACATTTTATGAAGGACTTAACAGACATCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G49810.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 1
tatatctctaacatcccattgctgcagatattggctaccttatgttcaggaaaccattcttgtatcagacaccaacatatctttatatttttttctatagGCTTTCAGTCCAGGAAAAAGTTAACCATGATGGTCATTCCTAGTATTTTTATTCCAGAAGACTGGTCATTTACATTTTATGAAGGACTTAACAGACATCC
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-----------------------gtatgtatg---tattgtatgtatttcccttttccctattgtctatctttttcctcgcta-atgcattgcattgcagGACATCACGGCAGAAACAAATTGACTATGATGGTCATTCCAAGCATTTTTCTACCCGAAGACTGGTCATTCACTTTTTACGAAGGGATTAATAGACATCC
upper sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 1
tatatctctaacatcccattgctgcagatattggctaccttatgttcaggaaaccattcttgtatcagacaccaacatatc-tttatatttttttctatagGCTTTCAGTCCAGGAAAAAGTTAACCATGATGGTCATTCCTAGTATTTTTATTCCAGAAGACTGGTCATTTACATTTTATGAAGGACTTAACAGACATCC
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-----------------------------------------gtatgtatgta--cgttttgcctttacctattattgtctcgctaatgcattgcattgcagGGCATCACGGGAGAAACAAATTGACTATGATGGTCATTCCAAGCATTTTTCTCCCCGAAGACTGGTCCTTCACTTTTTACGAAGGCATTAATAGACATCC
upper sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 2
---tatatctctaacatcccattgctgcagatattggctaccttatgttcaggaaaccattcttgtatcagacaccaacatatctttatatttttttctatagGCTTTCAGTCCAGGAAAAAGTTAACCATGATGGTCATTCCTAGTATTTTTATTCCAGAAGACTGGTCATTTACATTTTATGAAGGACTTAACAGACATCC
||| ||| | ||| || | ||| | | | |||| | | || ||| || | | | | | | || | || ||||| ||||| || || || |||||||| || ||||| |||||||| |||||||||||||| ||||| ||||||||||| || |||||||||||
ttttatttctgttttatctgatgattaaggattactgatgtggt-tgtttattgtccgat--ttgaattaactgttttgacacttctcttttacatgctgcagGCTACTGCGGGAGGAAGAAATTGACAATGATGGTGATCCCTAGCATTTTTATCCCAGAAGACTGGTCCTTTACTTTTTATGAAGGTCTGAACAGACATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaggaaaccattcttgtatcagacaccaacatatctttatatttttttctatagGCTTTCAGTCCAGGAAAAAGTTAACCATGATGGTCATTCCTAGTATTTTTATTCCAGAAGACTGGTCATTTACATTTTATGAAGGACTTAACAGACATCC
tctttatatttttttc CT-rich tract
aacatatctttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatatctctaacatcccattgctgcagatattggctaccttatgttcaggaaaccattcttgtatcagacaccaacatatctttatatttttttctatagGCTTTCAGTCCAGGAAAAAGTTAACCATGATGGTCATTCCTAGTATTTTTATTCCAGAAGACTGGTCATTTACATTTTATGAAGGACTTAACAGACATCC
- - - - - -catccca
- - - - - - - - - - - - - - - - - - - - - - - caggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaccaa