Sequence
atgc intronic sequence ATGC exonic sequencegtaataatcatcttctctttaatgggtcttcgtcaaaatttgaaattttgaactttaactttctgtttgacatgaatctgttgacacctgagttttgtgtagtttgtaattttaactctatatttggtggatttttgttcgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGAGTGCGTCCAAAGAGATTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
Basic information
species | Glycine max |
transcript | GLYMA19G43630.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g43700.1 (Oryza sativa), 3'ss of exon 1
gtaataatcatcttctctttaatgggtcttcgtcaaaatttgaaattttgaactttaactttctgtttgacatgaatctgttgacacctgagttttgtgtagtttgtaattttaactctatatttggtggatttttgttcgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGAGTGCGTCCAAAGAGATTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
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---------------------------------------------gcatgcagtaaacatcaggatgtgcgatgactagctacatcctcagatttttt----tttactagtctaatcagttagttaatctggccttacactaatttc----agGCAGATGGTTGGATTGTGAGTCATATAACGTTACTGGCCAATCCTAATCAAGTGAGGCCAAAGAGATTTTGGGGCGTCTACACCAAGCTTAAGATATTCA
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G166903_T02 (Zea mays), 3'ss of exon 1
gtaataatcatcttctctttaatgggtcttcgtcaaaatttgaaattttgaactttaactttctgtttgacatgaatctgttgacacctgagttttgtgtagtttgta--attttaactctatatttggtggatttttgttcgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGAGTGCGTCCAAAGAGATTTTGGGGTGTCTACACAAAGCTCAAAATATTTA----
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--------------------------------------------------------agcttttatgttttcttgagttcg--gacattcaagtcatgtagatcttgtgccagtctgatgtggtagcgaagctgaccttgcatatatttcatca-ggcagACGGTTGGATCGTGAATCGTATAACGTTACTGGCTAATCCTAATCAATTTAGGCCAAAGAGGTTTTGGGGCGTCTACACCAAGCTGAAGATATTTAACAT
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G166903_T01 (Zea mays), 3'ss of exon 1
gtaataatcatcttctctttaatgggtcttcgtcaaaatttgaaattttgaactttaactttctgtttgacatgaatctgttgacacctgagttttgtgtagtttgta--attttaactctatatttggtggatttttgttcgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGAGTGCGTCCAAAGAGATTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
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----------------------------------------------------tagtagcttttatgttttcttgagttcg--gacattcaagtcatgtagatcttgtgccagtctgatgtggtagcgaagctgaccttgcatatatttcatca-gGCAGACGGTTGGATCGTGAATCGTATAACGTTACTGGCTAATCCTAATCAATTTAGGCCAAAGAGGTTTTGGGGCGTCTACACCAAGCTGAAGATATTTA
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaataatcatcttctctttaatgggtcttcgtcaaaatttgaaattttgaactttaactttctgtttgacatgaatctgttgacacctgagttttgtgtagtttgtaattttaactctatatttggtggatttttgttcgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGAGTGCGTCCAAAGAGATTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
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---------gtttggtttttattgtctagttatagtagtttaaagatctaaa---gagttctcctttcgat-tgagtttg-----agcttaaatttg-atcacatactgctttg--tttaaagttgtttgcttttgattc--------tatagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAAGTTCATCCGACTAGGTTCTGGGGTGTTTATACAAAGCTTAAGATCTTTA
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 1
gtaataatcatcttctctttaatgggtcttcgtcaaaatttgaaattttgaactttaactttctgtttgacatgaatctgttgacacctgagttttgtgtagtttgtaattttaactctatatttgg-tggatttttgttcgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGAGTGCGTCCAAAGAGATTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
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--------------------------------------------------agagacagttgaatgtttgacta----ctgctgctattttactgtgattgtttttacttatctaatattctttggggatcggttctggtgaatattgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|213620033|gb|DB965367.1|DB965367EST: TCGTGTTGGTCTCCGATGGTGTGTCTGATTATGCCAAAAGCCTACTCCGG GCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGA
genomic: TCGTGTTGGTCTCCGATGGTGTGTCTGATTATGCCAAAAGCCTACTCCGGgtaataatca ... ttttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGA
EST:
gi|213606612|gb|DB972533.1|DB972533EST: TCGTGTTGGTCTCCGATGGTGTGTCTGATTATGCCAAAAGCCTACTCCGG GCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGA
genomic: TCGTGTTGGTCTCCGATGGTGTGTCTGATTATGCCAAAAGCCTACTCCGGgtaataatca ... ttttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagtttgtaattttaactctatatttggtggatttttgttcgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGAGTGCGTCCAAAGAGATTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
ttttaac putative branch site (score: 2)
ttgtaattttaactct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataatcatcttctctttaatgggtcttcgtcaaaatttgaaattttgaactttaactttctgtttgacatgaatctgttgacacctgagttttgtgtagtttgtaattttaactctatatttggtggatttttgttcgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGAGTGCGTCCAAAGAGATTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA