Sequence
atgc intronic sequence ATGC exonic sequencegtatctacgtccagaaccctttgtttggaaatcttcaaagtgtcgacaaggtttttcaacagtctacacctttcatttcagaattgtcgtttgatatctgctataattcgttggtgacagGCTCTTGCTAAGCTGGTAGCAGTTTGTGGTCCCTATCATCGGATGACAGCGGGAGCCTACAGCCTCCTTGCTGTAGTTTTATATCATACTGGAGACTTCA
Basic information
species | Glycine max |
transcript | GLYMA16G02770.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 15
gtatctacgtccagaaccctttgtttggaaatcttcaaagtgtcgacaaggtttttcaacagtctacac-ctttcatttcagaattgtcgtttgatatctgctataattcgttggtgacagGCTCTTGCTAAGCTGGTAGCAGTTTGTGGTCCCTATCATCGGATGACAGCGGGAGCCTACAGCCTCCTTGCTGTAGTTTTATATCATACTGGAGACTTCA
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----------------------------gtatcctct-----ttcacaaaacagtctatctttttgaacatttttggatgccatttgttttttaatcactattccaatggatgaatg-cagGCTCTTGCTAAACTCATAACAGTTTGTGGTCCCTATCATCGAATGACAGCTGGAGCTTATAGTCTGCTAGCTGTTGTATTGTATCACACTGGTGATTTTA
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 17
gtatctacgtccagaaccctttgtttggaaatcttcaaagtgtcgacaaggtttttcaacagtctacacctttcatttcagaattgtcgtttgatatctgctataattcgttggtgacagGCTCTTGCTAAGCTGGTAGCAGTTTGTGGTCCCTATCATCGGATGACAGCGGGAGCCTACAGCCTCCTTGCTGTAGTTTTATATCATACTGGAGACTTCA
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--gtccatgtcta---ctcctcagct--atttcttcatatt----acttgttttttatacagcgtcatgattttgttt------tgttgttttgtctct-ttctttttttcctccattagGCTCTTGCTAAACTCGTAGCAGTTTGCGGTCCCTATCACAGAATGACAGCCGGAGCTTACAGTTTACTTGCTGTGGTTCTATATCACACTGGTGACTTTA
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 17
gtatctacgtccagaaccctttgtttggaaatcttca------aagtgtcgacaaggtttttcaacag------tctacacct-ttcatttcagaattgtcgtttgatatctgctataattcgttggtg---acagGCTCTTGCTAAGCTGGTAGCAGTTTGTGGTCCCTATCATCGGATGACAGCGGGAGCCTACAGCCTCCTTGCTGTAGTTTTATATCATACTGGAGACTTCA
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gtatttgatttaaaagtccatcggtttgtcatttctatatgtaaactaccaatcgggtgcagcagaaaaatctttctttgcctgttcattggtaaatta--atatgctaccttttgtatttttgtggtttttgcagGCTCTGGCAAAGCTGGTCGCAGTTTGTGGTCCCTACCATCGAATGACAGCAGGAGCTTACAGCCTCCTTGCTGTAGTTTTGTATCATACAGGGGACTTCA
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 2
gtatctacgtccagaaccctttgtttggaaatcttca------aagtgtcgacaaggttt--ttcaacagtctacacct-----ttcatttcagaattgtcgtttgatatctgctataattcgttggtg---acagGCTCTTGCTAAGCTGGTAGCAGTTTGTGGTCCCTATCATCGGATGACAGCGGGAGCCTACAGCCTCCTTGCTGTAGTTTTATATCATACTGGAGACTTCA
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gtatttgatttaaaagtccatcggtttgtcatttctatatgtaaactaccaatcgggtgcagtagaaaaatctttctttgcatgttcattggtaaatta--atatgctatcttttgtatttttgtggtttttgcagGCTCTGGCAAAGCTGGTCGCAGTTTGTGGTCCCTACCATCGAATGGCAGCAGGAGCTTACAGCCTCCTTGCTGTAGTTTTGTATCATACAGGGAACTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacctttcatttcagaattgtcgtttgatatctgctataattcgttggtgacagGCTCTTGCTAAGCTGGTAGCAGTTTGTGGTCCCTATCATCGGATGACAGCGGGAGCCTACAGCCTCCTTGCTGTAGTTTTATATCATACTGGAGACTTCA
gtttgat putative branch site (score: 5)
tataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctacgtccagaaccctttgtttggaaatcttcaaagtgtcgacaaggtttttcaacagtctacacctttcatttcagaattgtcgtttgatatctgctataattcgttggtgacagGCTCTTGCTAAGCTGGTAGCAGTTTGTGGTCCCTATCATCGGATGACAGCGGGAGCCTACAGCCTCCTTGCTGTAGTTTTATATCATACTGGAGACTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA