Sequence
atgc intronic sequence ATGC exonic sequence...atttccaatagataggggtcacaagtacaatgcctgttttcactctcttcatcccattgtctagaaaatagagaattactaattaccttgttttcaccagGTTCTATTATGCTATGGAACTTACACAAATTTGGAGCTTCTTGAACACTATGGGTTTCTCCTACAAGAAAATCCAAATGACAAAGTTTTTATCCCTTTGG
Basic information
species | Glycine max |
transcript | GLYMA14G39060.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G39060.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G17240.1 (Arabidopsis thaliana), 3'ss of exon 5
------atttccaatagataggggtcacaagtacaatgcctgttttcactctcttcatcccattgtctagaaaatagagaattacta--attaccttgttttcaccagGTTCTATTATGCTATGGAACTTACACAAATTTGGAGCTTCTTGAACACTATGGGTTTCTCCTACAAGAAAATCCAAATGACAAAGTTTTTATCCCTTTGG
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gtacaagtcctcaactagcttttgttacagctgcgaaactaatg-----aagcggaagcacaacgtagaaaatatactgaatggtgaggattgtatttgtgggtgtagGTTCTTCTATGTTATGGGACTTACACGAATCTAGAGCTTCTTGAGCACTATGGGTTTATGTTAGAAGAGAACTCAAATGACAAGGTCTTCATTCCTCTAG
upper sequence: GLYMA14G39060.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0079g00650.t01 (Vitis vinifera), 3'ss of exon 1
----atttccaatagataggggtcacaagtacaatgcctgttttcactctcttcatcccattgtctagaaaatagagaattactaattaccttgttt-tcaccagGTTCTATTATGCTATGGAACTTACACAAATTTGGAGCTTCTTGAACACTATGGGTTTCTCCTACAAGAAAATCCAAATGACAAAGTTTTTATCCCTTTGG
| || || || ||| | | ||| ||| || ||| ||| || | | | || ||| | || | | |||||||| ||| |||||||||| ||||| |||||||| ||||||||||||||||||||||| || | ||||| |||||||| || | ||| || || ||||
tcctacttagtgccaat-ggcatcatcatcattttgcatgtcttgttggccttt----catatatgaggcgacatgggtttgaaaataaagttacatgtttgcagGTTCTTTTAAGCTATGGAACATACACGAATTTGGAACTTCTTGAACACTATGGGTTTCTTTTAGATGAAAACCCAAATGATAAGGCTTTCATTCCCTTGG
upper sequence: GLYMA14G39060.2 (Glycine max), 3'ss of exon 4
lower sequence: PP1S59_346V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------------atttccaa--tagataggggtcacaagtacaatgcctgttttcactctcttcatccc-------attgtctagaaaatagagaattactaattacct--------tgttt---tcaccagGTTCTATTATGCTATGGAACTTACACAAATTTGGAGCTTCTTGAACACTATGGGTTTCTCCTACAAGAAAATCCAAATGACAAAGTTTTTATCCCTTTGG
| ||| | |||| || || || ||| || | | || || | || || | | | | | |||| | || || | |||||||| | ||||||||||| |||||||| | ||||||||||| |||||||| ||||| |||| || || |||||||||||| || |
gtaagctctgccacacacagcgctgccatacttaaatacgttacgtttgtcgtgtgcaagccaaacctccacaacatagttctgaattagacagccttctcagaggagtggccccattgctcctcagcgatgaggactgaaatgggcttaaatagacttagtattcatttacgtgtgggaggtggttggttttgcagGTTCTGCTGTGCTATGGAACGTACACAAACCTTGAGCTTCTTGAGCACTATGGATTTCTACTACCTTTCAACCCCAATGACAAAGTTCACATAGAACTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcatcccattgtctagaaaatagagaattactaattaccttgttttcaccagGTTCTATTATGCTATGGAACTTACACAAATTTGGAGCTTCTTGAACACTATGGGTTTCTCCTACAAGAAAATCCAAATGACAAAGTTTTTATCCCTTTGG
tactaat putative branch site (score: 1)
ccttgttttc putative PPT
aaaatagagaattact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttccaatagataggggtcacaagtacaatgcctgttttcactctcttcatcccattgtctagaaaatagagaattactaattaccttgttttcaccagGTTCTATTATGCTATGGAACTTACACAAATTTGGAGCTTCTTGAACACTATGGGTTTCTCCTACAAGAAAATCCAAATGACAAAGTTTTTATCCCTTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - -caatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taccttg