Sequence
atgc intronic sequence ATGC exonic sequence...ttttttaccacccttattgcttctccctttgttaatttttctgttgaattgttttcatatatcaagaattaatacttgcatattttcttcttctatgcagGTATTCGTGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
Basic information
species | Glycine max |
transcript | GLYMA18G45720.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g22640.1 (Oryza sativa), 3'ss of exon 4
ttttttaccacccttattgcttctccctttgttaatttttctgttgaattgttttcatatatcaagaattaatac-ttgcatattttcttcttctatgcagGTATTCGTGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
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cttagggatgccccactaagctatgttttgtttagcatcttgatcatgttaatgcaatac-taaataactgagacatcacgttttgtcatgttgtgtaaagGTATTCGCATTCAAAATATTCAGCCAGGCCAAATCATAATGGATATAGATCTTCGTTGGGGTGGTGATCCAAGCATAATCCTTGCTGTTGATGCTGTTGT
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092129_T02 (Zea mays), 3'ss of exon 4
ttttttaccacccttattgcttctccctttgtt--aatttttctgttgaattgttttcatatatcaagaattaata---cttgcatattttct-tcttctatgcagGTATTCGTGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
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------cccttttttattgcatttatatctgcttgaatcttgatgcaggactacataagtgcttaaaaaaatgatgggttttgtttgtttgttgtgatttgcgaagGTATTCGTATTCAAAATCTTCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGT
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G61050.1 (Arabidopsis thaliana), 3'ss of exon 5
ttttttaccacccttattgcttctcc---ctttgttaatttttctgttgaattgttttcatatatcaagaattaatacttgcatattttcttcttctatgcagGTATTCGTGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
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atgctaatgaatccttgtgcttgaaagaacatcatgcagttgtctcttaggttagttt--tgctgtaagcctgagcatatgcataataaatcattgt-tgcagGTATTCGTGTTCAAAGTTTCAAGGAAGGTCAAGTCACAATGGACGTTGATCTTCGATGGGGTGGTGATCCAAATATTGTTTTAGGTGTGACAGCACTTGT
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0048g01410.t01 (Vitis vinifera), 3'ss of exon 5
ttttttaccacccttattgcttctccctttgttaatttttctgttgaattgtttt-catatatc---aagaattaatacttgcatattttcttcttctatgcagGTATTCGTGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
| | | | | || | | | || | ||| | ||| | || || ||| | |||||||| || || || ||||||| ||||||||||| || ||||| ||||| ||||| |||||||| || || || || |||||||||||||| | ||| |||| ||||||||||| | |
----ccaattcacatgtcgccatatgaaagttcagcctgccttataaatcacaatgcatttgtctttgagcatttgtgcttgcataattactgaatcaatgcagGAATTCGTGTTCAAAGCCTTAAGAAAGGGCAAATTATAATGGATATCGACTTGCGATGGGGTGGTGATCCAAGCATTATTTTAGCTGTTGAAGCTGCTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattgttttcatatatcaagaattaatacttgcatattttcttcttctatgcagGTATTCGTGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
aattaat putative branch site (score: 3)
catattttcttcttct putative PPT
ttttcatatatcaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttttaccacccttattgcttctccctttgttaatttttctgttgaattgttttcatatatcaagaattaatacttgcatattttcttcttctatgcagGTATTCGTGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - caccctt
- - - - - - - - - - ttctccc
- - - - - - - - - - - - - - - - - - - -tctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacttgc