Sequence
atgc intronic sequence ATGC exonic sequencegtaagttacttgtgcctgttgttgttcctctgtatatcatatatcttgccatttctttgttattttctgttgcttctttcttttcttgtacctaatgatttgcatatatatatatgctctcatattgccagGCACCTCAAGGTGTTCATGTGGTCTGTAAAAGATTTCCAAGAATAAAAATCCTGACATCTGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
Basic information
species | Glycine max |
transcript | GLYMA14G01480.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 14
gtaagttacttgtgcctgttgttgttcctctgtatatcatatatcttgccatttctttgttattttctgttgcttctttcttttcttgtacctaatgatttgcatatatatatatgctctcatattgccagGCACCTCAAGGTGTTCATGTGGTCTGTAAAAGATTTCCAAGAATAAAAATCCTGACATCTGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
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---------------------------ctgtacatgcttgctatgttggaacttatca--cgttcgctgtta-ttgtgtggcggttgataaccattgagcttaccacaaaaac-tgttggaattgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G26510.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaagttacttgtgcctgttgttgttcctctgtatatcatatatcttgccatttctttgttattttctgttgcttctttcttttcttgtacctaatgatttgcatatatatatatgctctcatattgccagGCACCTCAAGGTGTTCATGTGGTCTGTAAAAGATTTCCAAGAATAAAAATCCTGACATCTGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
| || | ||| || |||||| ||| || || | ||| | | | | | ||| | | | | | | | |||| | | | || | | ||||||||||||||||||||||||||||| |||| ||| ||||||||||| || |||||||||| || || | ||| || || ||||| || ||||| || |
---------gtaagc-taacacacaccctttgcgtatcatttatacacccctt--gtgattactccttatc-catgtttatccacaagaatgcagctggattgagatattttttttcttt-gttcaatcagGCACCTCAAGGTGTTCATGTGGTCTGCAAAAAATTCCCAAGAATAAAGATAGTGACATCTGAAATCGATAATGGGTTAAACGAAGAGTTTCGTGTTATTC
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 14
gtaagttacttgtgcc--tgttgttgttcctctgtatatcatatatcttgccatttctt----tgttattttctgttgct-tctttcttttcttgtacctaa----tgatttgcatatatatatatgctctc---atattgccagGCACCTCAAGGTGTTCATGTGGTCTGTAAAAGATTTCCAAGAATAAAAATCCTGACATCTGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
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gtaagcccatgtagcccttgttgctattcgtttttgtatcacacttgaactcattataaaaagtttgacttttggctgctctccttcccatggtccactggagctttgatattcatatagctgtaatctgtctaaatcttaccagGCACCTCAGGGAGTGCATGTGGTCTGCAAAAGCTTCCCGAGGATAAAGATTGTAACATCTGAGATTGATGTTGGTCTGAATGAAGATTTCCGTGTCATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttttcttgtacctaatgatttgcatatatatatatgctctcatattgccagGCACCTCAAGGTGTTCATGTGGTCTGTAAAAGATTTCCAAGAATAAAAATCCTGACATCTGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
acctaat putative branch site (score: 3)
ctctcat putative PPT
taatgatttgcatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttacttgtgcctgttgttgttcctctgtatatcatatatcttgccatttctttgttattttctgttgcttctttcttttcttgtacctaatgatttgcatatatatatatgctctcatattgccagGCACCTCAAGGTGTTCATGTGGTCTGTAAAAGATTTCCAAGAATAAAAATCCTGACATCTGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA