Sequence
atgc intronic sequence ATGC exonic sequence...catttttagtttttccaagtattgatttctgctcctcattatgtgaaccttgatctaatgctggaatctatctttccttcataatttcttctccttgaagGTTGCTAGCCAAGAGACATATGGAACCTTGGGTGCTATTGTCAGAAGCCGATCAGGAAATAGAGAAGTTGGTTTTCTAACAAATCGACATGTAGCTGTTG
Basic information
species | Glycine max |
transcript | GLYMA20G02500.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G35155.1 (Arabidopsis thaliana), 3'ss of exon 3
catttttagtttttccaagtattgatttctgctcctcattatgtgaaccttgatctaatgctggaatct-atctttccttcataatttcttctccttgaagGTTGCTAGCCAAGAGACATATGGAACCTTGGGTGCTATTGTCAGAAGCCGATCAGGAAATAGAGAAGTTGGTTTTCTAACAAATCGACATGTAGCTGTTG
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--------------gtacatcgttgttttttccttccatcttctgcaaccta---taagcgtaaagtctcagttttgtttcatgttgtgt---------agGTTGCAAGCCAAGAAACATATGGAACCTTGGGAGCTATAGTGAAAAGCAGAACAGGTAACCACCAGGTTGGTTTCCTTACCAATCGGCATGTCGCAGTTG
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G45030.2 (Arabidopsis thaliana), 3'ss of exon 3
catttttagtttttccaagtattgatttctgctcctcattatgtgaaccttgatctaatgctggaatctatctttccttcataatttcttctccttgaagGTTGCTAGCCAAGAGACATATGGAACCTTGGGTGCTATTGTCAGAAGCCGATCAGGAAATAGAGAAGTTGGTTTTCTAACAAATCGACATGTAGCTGTTG
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-----gtaatttgt----gtactaaact-tgcatatacgcttgt-attatcgac--aatattacaata-atcatctggccatgcctc--tcatcttgtagGTGGCTAGCCAAGAGACATATGGAACCTTAGGTGCAATTGTAAAGAGTAAAACTGGTATCAGACAGGTTGGTTTCCTAACAAACCGGCATGTTGCAGTTG
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g01870.t01 (Vitis vinifera), 3'ss of exon 4
--catttttagtttttc--caagtattgatttctgctcctcattatgtgaaccttgatctaatgctggaatctatctttccttcataatttcttctccttgaagGTTGCTAGCCAAGAGACATATGGAACCTTGGGTGCTATTGTCAGAAGCCGATCAGGAAATAGAGAAGTTGGTTTTCTAACAAATCGACATGTAGCTGTTG
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tacacctgaaccttgtcaacaggaatctgtttacacattccattgcttgcatcttcatc-attgct---ttttcaaattgcccaattgcttcttgttcatgcagGTTGCAAGCCAAGAGACATACGGAACCTTGGGTGCTATTGTAAAAAGCCGAACAGGAAACCAACAGGTTGGTTTCCTCACAAATCGGCACGTGGCAGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccttgatctaatgctggaatctatctttccttcataatttcttctccttgaagGTTGCTAGCCAAGAGACATATGGAACCTTGGGTGCTATTGTCAGAAGCCGATCAGGAAATAGAGAAGTTGGTTTTCTAACAAATCGACATGTAGCTGTTG
atctaat putative branch site (score: 3)
tctatctttccttcat putative PPT
ttcataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttttagtttttccaagtattgatttctgctcctcattatgtgaaccttgatctaatgctggaatctatctttccttcataatttcttctccttgaagGTTGCTAGCCAAGAGACATATGGAACCTTGGGTGCTATTGTCAGAAGCCGATCAGGAAATAGAGAAGTTGGTTTTCTAACAAATCGACATGTAGCTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - ccaagta
- - - - - - - - - - - - - - -tgctcct
- - - - - - - - - - - - - - - - - - - - -tgtgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgga