Sequence
atgc intronic sequence ATGC exonic sequencegtatcactgaaacacgctgcgcatttagtttcactgtttatactcaggagtttgttcaatgagttacttagaaaagattgcacaaaaagtatttcagttatacatcaagtttctgttgagtcttttctcctatactgagttgtttatttcatataacaatttttaactttatgtaaataaatttagGTGAAAAGTGAATTGCCAAGTACCTTCAAAGCCTATCGTTATCAGCAGCACAGGTGGTCATGTGGCCCAGCTAATCTTTTCAAGAAAATGGCAATGGAAA
Basic information
species | Glycine max |
transcript | GLYMA20G32990.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G32990.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0074g00500.t01 (Vitis vinifera), 3'ss of exon 5
gtatcactgaaacacgctgcgcatttagtttcactgtttatactcaggagtttgttcaatgagttacttagaaaagattgcacaaaaagtatttcagttatacatcaagtttctgttgagtcttttctcctatactgagttgtttatttcatataacaatttttaactttatgtaaataaattt--agGTGAAAAGTGAATTGCCAAGTACCTTCAAAGCCTATCGTTATCAGCAGCACAGGTGGTCATGTGGCCCAGCTAATCTTTTCAAGAAAATGGCAATGGAAA
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-----------------------------------------------------gtatggtttattacccatatgaga---------acatgcttca-tcccaaaacattttgtaggaaagccttctt----------agttgtttctatatggacctgattgtaaacgctaaatcaatatacttctagGTGAAAAATGAGTTGCCCAGTACTTTCAAAGCCTACCGCTATCAGCAGCATAGGTGGTCTTGTGGTCCTGCTAATCTCTTCAAGAAAATGGCAATAGAAA
upper sequence: GLYMA20G32990.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ17366 (Selaginella moellendorffii), 3'ss of exon 5
gtatcactgaaacacgctgcgcatttagtttcactgtttatactcaggagtttgttcaatgagttacttagaaaagattgcacaaaaagtatttcagttatacatcaagtttctgttgagtcttttctcctatactgagttgtttatttcatataacaatttttaactttatgtaaataaatttagGTGAAAAGTGAATTGCCAAGTACCTTCAAAGCCTATCGTTATCAGCAGCACAGGTGGTCATGTGGCCCAGCTAATCTTTTCAAGAAAATGGCAATGGAAA
| ||| ||| || |||| || ||| | ||| | ||| || | | | | ||||||| | || | || ||||| || || ||||||||||||||||||||||| ||||||||||| || ||||| || || ||| ||| ||
--------------------------------------------------------------------------------------------------------------gtacgtttagtaccttttcct---------tgcttagagtaagtaatatggttt--ctctgttt-------ctcagGTGAAGAACGAGCTTCCCAGTACATTTAAGGCCTATCGTTATCAGCAGCACAGATGGTCATGTGGGCCGGCTAACCTCTTTCGGAAGATGATTCCGGGGG
upper sequence: GLYMA20G32990.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ35401 (Selaginella moellendorffii), 3'ss of exon 5
gtatcactgaaacacgctgcgcatttagtttcactgtttatactcaggagtttgttcaatgagttacttagaaaagattgcacaaaaagtatttcagttatacatcaagtttctgttgagtcttttctcctatactgagttgtttatttcatataacaatttttaactttatgtaaataaatttagGTGAAAAGTGAATTGCCAAGTACCTTCAAAGCCTATCGTTATCAGCAGCACAGGTGGTCATGTGGCCCAGCTAATCTTTTCAAGAAAATGGCAATGGAAA
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--------------------------------------------------------------------------------------------------------------gtacgtttggtaccttttcct---------tgcttagagtaagtaatatggttt--ctctgttt-------ctcagGTGAAGAACGAGCTTCCCAGTACATTTAAGGCCTATCGTTATCAGCAGCACAGATGGTCATGTGGGCCGGCTAACCTCTTTCGGAAGATGATTCCGGGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atactgagttgtttatttcatataacaatttttaactttatgtaaataaatttagGTGAAAAGTGAATTGCCAAGTACCTTCAAAGCCTATCGTTATCAGCAGCACAGGTGGTCATGTGGCCCAGCTAATCTTTTCAAGAAAATGGCAATGGAAA
ttttaac putative branch site (score: 2)
tttatttcatataaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcactgaaacacgctgcgcatttagtttcactgtttatactcaggagtttgttcaatgagttacttagaaaagattgcacaaaaagtatttcagttatacatcaagtttctgttgagtcttttctcctatactgagttgtttatttcatataacaatttttaactttatgtaaataaatttagGTGAAAAGTGAATTGCCAAGTACCTTCAAAGCCTATCGTTATCAGCAGCACAGGTGGTCATGTGGCCCAGCTAATCTTTTCAAGAAAATGGCAATGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA