Sequence
atgc intronic sequence ATGC exonic sequencegtatggataatttcttccatctcggtgttcggtttgttcctgaagccaacaaccaaatttaccaacattttgcattgaatcttgaagGCACTCTCAAAATTAGTGTCAGTTTGTGGGCCTTACCATAGAATGACAGCAGGAGCATATAGTCTCTTGGCTGTAGTGTTGTACCATACTGGAGATTTCA
Basic information
species | Glycine max |
transcript | GLYMA04G24430.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G318635_T01 (Zea mays), 3'ss of exon 16
----gtatggata-atttcttccatctcggtgttcggtttgttcctgaa--gccaacaaccaaatttaccaacat-----tttgcattgaatcttgaagGCACTCTCAAAATTAGTGTCAGTTTGTGGGCCTTACCATAGAATGACAGCAGGAGCATATAGTCTCTTGGCTGTAGTGTTGTACCATACTGGAGATTTCA
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gtacgattcgttatattactattgcatccatatgtgaagaattcttgaactggtgcttctttcggtttccatcattctaatctgcacatgattgtgcagGCTCTTGCAAAACTTGTTGCTGTTTGTGGTCCTTATCATAGAATGACGGCAGGAGCATACAGCCTTCTTGCAGTAGTGCTTTATCATACTGGTGACTTCA
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 16
gtatggataatttcttcc-----atctcggtgttc----ggtttgttcctg---aagccaacaaccaaattta-ccaacattttgcattgaatcttgaagGCACTCTCAAAATTAGTGTCAGTTTGTGGGCCTTACCATAGAATGACAGCAGGAGCATATAGTCTCTTGGCTGTAGTGTTGTACCATACTGGAGATTTCA
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gcaaggataattttgtttctgaaacttttgttttacatggatgtatttatgtttgttcaaatggtctaactaagctgattttctgggatgaactccatagGCATTGGCCAAGCTTGTAGCTGTGTGCGGCCCATATCATAGAATGACCGCTGGAGCGTATAGTCTTCTCGCTGTTGTGCTGTACCATACTGGGGATTTTA
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv11s0037g00840.t01 (Vitis vinifera), 3'ss of exon 16
gtatgga-taatttcttccatctcggtgtt------cggtttgttcctgaagccaacaaccaaatttaccaacattttgcattgaatcttgaagGCACTCTCAAAATTAGTGTCAGTTTGTGGGCCTTACCATAGAATGACAGCAGGAGCATATAGTCTCTTGGCTGTAGTGTTGTACCATACTGGAGATTTCA
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gtaaagaacaatatctctccttttgaagttgtatgctggtcttatactaaatctgataactacttggaccaatttgctttgctgaattttgaagGCACTCTCAAAACTTGTGGCAGTCTGTGGTCCTTATCATCGAATGACAGCTGGAGCATATAGTCTTTTGGCTGTAGTGCTCTACCATACTGGGGATTTTA
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ08067 (Selaginella moellendorffii), 3'ss of exon 16
gtatggataatttcttccatctcggtgttcggtttgttcctgaagccaacaaccaaatttac-caacattttgcattgaat-cttgaagGCACTCTCAAAATTAGTGTCAGTTTGTGGGCCTTACCATAGAATGACAGCAGGAGCATATAGTCTCTTGGCTGTAGTGTTGTACCATACTGGAGATTTCA
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-----------------------------------------gtaaatctctaccattctcgtacatttttctctaatgtttgtttgtagGCCCTGACAAAATTGATAGCTGTTTGCGGGCCTTACCATCGAATGACTGCTGGAGCATATAGTTTGCTTGCAGTGGTTCTTTACCACACAGGAGACTTCA
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 16
gtatggataatttcttccatctcggtgttcggtttgttcctgaagccaacaaccaaatttac-caacattttgcattgaat-cttgaagGCACTCTCAAAATTAGTGTCAGTTTGTGGGCCTTACCATAGAATGACAGCAGGAGCATATAGTCTCTTGGCTGTAGTGTTGTACCATACTGGAGATTTCA
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-----------------------------------------gtaaatctctaccactctcgtacatttttctctaatgtttgtttgtagGCTCTGACAAAATTGATAGCTGTTTGCGGGCCTTACCATCGAATGACTGCTGGAGCATATAGTTTGCTTGCAGTGGTTCTTTACCACACAGGAGACTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttcctgaagccaacaaccaaatttaccaacattttgcattgaatcttgaagGCACTCTCAAAATTAGTGTCAGTTTGTGGGCCTTACCATAGAATGACAGCAGGAGCATATAGTCTCTTGGCTGTAGTGTTGTACCATACTGGAGATTTCA
aaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggataatttcttccatctcggtgttcggtttgttcctgaagccaacaaccaaatttaccaacattttgcattgaatcttgaagGCACTCTCAAAATTAGTGTCAGTTTGTGGGCCTTACCATAGAATGACAGCAGGAGCATATAGTCTCTTGGCTGTAGTGTTGTACCATACTGGAGATTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT