Sequence
atgc intronic sequence ATGC exonic sequence...ctttctctttgcaatgtatgtgtttgtcttttcaagtagttttattacattactgtacttgcttcttacctgccaggttatcttctgttttctcatgcagGCTTATATTGAGAAAGAAGACAGTAAAAAGCTGAAGCAAAAGCAAAGAGAACGCATGCAACCAAAAATGGGGAAAATGGATATTGATTATCAG
Basic information
species | Glycine max |
transcript | GLYMA13G25110.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 6
----ctttctctttgcaatgtatgtgtttgtcttttcaagtagttttattacattactgtacttgcttcttacctgccaggttatcttc----tgttttctcatgcagGCTTATATTGAGAAAGAAGACAGTAAAAAGCTGAAGCAAAAGCAAAGAGAACGCATGCAACCAAAAATGGGGAAAATGGATATTGATTATCAG
||| | | | || | | | | || | | || | ||||| || ||| | | || | || | ||| | | ||||| ||||||||||| || || ||||||||| |||| |||||||| | || || ||||||||||||||||| || |||||||| |||||||||
gtaacttgattatctcgattcttttaggcttttcttgggaca-tgataccagcttactttaggagctgtgtggtgctcgaattttatttaaatttctttttttttcagGCATATATTGAGAAGGAGGATAGTAAAAAGTTGAAACAAAAGCAGCGGGAGCGTATGCAACCAAAAATGGGCAAGATGGATATAGATTATCAG
upper sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 2
-------------------------------ctttctctttgca-atgtatgtgtttgtcttttcaagtagtt----------ttattacattactgtact-tgcttcttacctgccaggttatcttctgttttctcatgcagGCTTATATTGAGAAAGAAGACAGTAAAAAGCTGAAGCAAAAGCAAAGAGAACGCATGCAACCAAAAATGGGGAAAATGGATATTGATTATCAG
| | ||| ||| || || | ||| ||||| | | | | ||| || | || | || | | | || || || |||| | | ||||| |||||||||||||| || || || ||| |||| || || || | || |||||||| || |||||||| ||||||||||| |||||||||
gtaacttgcttcttgtatctcagtaatttacttctttctctgcttattcatttttttttctttgtagagcgctgcggaactattcattccagtttggtgccatgatcatgagctacctaattgatttctaaatgtgtacacagGCGTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGGGAGCGCATGCAGCCCAAAATGGGCAAAATGGATATAGATTATCAG
upper sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 6
lower sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 5
ctttctctttgcaatgtatgtgtttgtcttttcaagtagttttattacattactgtacttgcttcttacctgccaggttat-cttctgtt-ttctcatgcagGCTTATATTGAGAAAGAAGACAGTAAAAAGCTGAAGCAAAAGCAAAGAGAACGCATGCAACCAAAAATGGGGAAAATGGATATTGATTATCAG
||| ||| ||| | | || | | || | || ||||||| ||| ||| | || ||| ||| |||| ||| ||||||| |||||||||||||| |||| || |||||||||||||| | || | ||||||||||||||||| || ||||| ||||| || |||
---------------gtaaaagttattctctatcaata--taaggtgcaagtcgctaaatgcttcta--ctgtcagctaattcttgtgtggttcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
upper sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 3'ss of exon 6
ctttctctttgcaat----gtatgtgtttgtcttttcaagtagttttattacattactgtact-tgcttcttacctgccaggttatcttctgttttctcatgcagGCTTATATTGAGAAAGAAGACAGTAAAAAGCTGAAGCAAAAGCAAAGAGAACGCATGCAACCAAAAATGGGGAAAATGGATATTGATTATCAG
| | | |||| || | || | | | | || | | ||| | ||| || | | ||||||| || | ||| |||||||||||| || |||||||| || ||||| ||||||||||| || ||| ||||| ||||| |||||||| ||||| || |||||||||
-tctatatttggaaattcaatctggactcagcatctttagacataacggccctactttgtgttatgccatgtatttaatattttatcttatgggctatca----gGCTTATATTGAAAAGGAAGACAGCAAGAAGCTTAAGCAAAAGCAGAGGGAAAAGATGCAGCCAAAGATGGGGAAGATGGACATAGATTATCAG
upper sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S98_7V6.1 (Physcomitrella patens), 3'ss of exon 6
---ctttctctttgcaatgtatgtgtttgtcttttcaagtagttttattacattactgtacttgcttcttacctgccaggttatcttctgttttctcatgcagGCTTATATTGAGAAAGAAGACAGTAAAAAGCTGAAGCAAAAGCAAAGAGAACGCATGCAACCAAAAATGGGGAAAATGGATATTGATTATCAG
| | | | | || | ||| | | | | | | | | | | || | || | | || | || || |||||||| |||||||| |||||||| || ||||| ||||||||||| || || ||||| || || ||||| || ||||| || |||||||||
tgagatcaatcgtactcaatcagaacttagtgatacaatttgctccgtagtcatgtcatgttatgtcatcaattga-atattttatgctatgggct-at-cagGCTTACATTGAGAAGGAAGACAGCAAGAAGCTCAAGCAAAAGCAGAGGGAGAAAATGCAGCCTAAGATGGGAAAGATGGACATCGATTATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacattactgtacttgcttcttacctgccaggttatcttctgttttctcatgcagGCTTATATTGAGAAAGAAGACAGTAAAAAGCTGAAGCAAAAGCAAAGAGAACGCATGCAACCAAAAATGGGGAAAATGGATATTGATTATCAG
ttcttac putative branch site (score: 2)
ttatcttctgttttct putative PPT
ttatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttctctttgcaatgtatgtgtttgtcttttcaagtagttttattacattactgtacttgcttcttacctgccaggttatcttctgttttctcatgcagGCTTATATTGAGAAAGAAGACAGTAAAAAGCTGAAGCAAAAGCAAAGAGAACGCATGCAACCAAAAATGGGGAAAATGGATATTGATTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - ctttgca
- - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttctg