Sequence
atgc intronic sequence ATGC exonic sequencegtaagctacccctttttgcatgtatttatttctttaatcagtttccacaattgcatcttttatgcatctaactaaagtttctgtatgaaattaacgatgcagcacatctataaagttgcatgcttttttgtgtaattttcctgcaatgtttctcaagtttaatgtttcctgtgacagAAAGATGATCTCAAGATGGTGGTGTCACATTTAAGAAGCAACAAACAAGTATCTCGTATAGGACTTTGGGGACGATCAATGGGTGCTGTTACAAG
Basic information
species | Glycine max |
transcript | GLYMA09G02050.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 4
gtaagctacccctttttgcatgtatttatttctttaatcagtttccacaattgcatcttttatgcatctaactaaagtttctgtatgaaattaacgatgcagcacatctataaagttgcatgcttttttgtgtaattttcctgcaatgtttctcaagtttaatgtttcctgtgacagAAAGATGATCTCAAGATGGTGGTGTCACATTTAAGAAGCAACAAACAAGTATCTCGTATAGGACTTTGGGGACGATCAATGGGTGCTGTTACAAG
||| | | | | | | | | || || ||| || | | || | ||| | || | ||| || |||||| | |||||||| | |||||| ||| ||| ||| || |||| ||| | ||||| |||||||| |||||||||||||||||||||||
----------------------------------------------------------------------------------gtacatagtcatca------taattttttgaaaacacactcttattgttttgcaattgcactaatctgataaaaatacaatcactct-----cagAAACAGGATCTCAAATGCGCGGTGTCCTTTTTGCGAAACAATAAGGAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAG
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 4
gtaagctacccctttttgcatgtatttatttctttaatcagtttccacaattgcatcttttatgcatctaactaaagtttctgtatgaaattaacgatgcagcacatctataaagttgcatgcttttttgtgtaattttcctgcaatgtttctcaagtttaatgtttcctgtgacagAAAGATGATCTCAAGATGGTGGTGTCACATTTAAGAAGCAACAAACAAGTATCTCGTATAGGACTTTGGGGACGATCAATGGGTGCTGTTACAAG
| | ||| || | || | || | | | || || | || | | | | | ||| || ||||||| || || || ||||||||| | || | | || || ||||| || ||||||| |||||||| ||||| |||||||||||||||||
--------------------------------------------------------------------------------------------------gtatataatcagtatcacttt-tgttcttctacatttatatcatggataattacattattctgaaattttct-----agAAAGAGGACCTAAAATGTGTGGTGTCATACCTACGGACCACTAAGCAAGTTTCCTGTATAGGCCTTTGGGGGCGATCGATGGGTGCTGTTACAAG
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G092895_T01 (Zea mays), 3'ss of exon 4
gtaagctacccctttttgcatgtatttatttctttaatcagtttccacaattgcatcttttatgcatctaactaaagtttctgtatgaaattaacgatgcagcacatctataaagttgcatgcttttttgtgtaattt-tcctgcaatgtttctcaagtttaatgtttcctgtgacagAAAGATGATCTCAAGATGGTGGTGTCACATTTAAGAAGCAACAAACAAGTATCTCGTATAGGACTTTGGGGACGATCAATGGGTGCTGTTACAAG
|| | | || || || |||| | | | || || |||| | ||||| || | | | | | | | | || |||| | |||||||| | ||||| | | | | || || ||||| ||| ||||||| ||||||||||| ||||||||||||||||||||
----------------------------------------------------------------------------gtgcgtacacactataaattttgtagca-------acattcatattctattttaaatggcaagtcctgaaaaatattaccactgtggtactccc------agAAGCAGGATCTCAAATGTGCTGTGTCCTTTCTGCGTAAGAATAAGCAAGTTTCTTGTATAGGTCTTTGGGGACGCTCAATGGGTGCTGTTACAAG
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 4
gtaagctacccctttttgcatgtatttatttctttaatcagtttccacaattgcatcttttatgcatctaactaaagtttctgtatgaaattaacgatgcagcacatctataaagttgcatgcttttttgtgtaattttcctgcaatgtttctcaagttt--aatgtttcctgtgacagAAAGATGATCTCAAGATGGTGGTGTCACATTTAAGAAGCAACAAACAAGTATCTCGTATAGGACTTTGGGGACGATCAATGGGTGCTGTTACAAG
|| | | || |||| || ||| | ||| | | ||| | | | | || ||||| || || || || | ||||||| || ||||| | ||||||| | | | ||| |||||||| || |||||| |||||||| |||||||||||||| |||||| |
----------------------------------------------------------------------------gtatataatcagtatcaacgttgttctttgcttatt---ctacattcatattttcggagatcac-----atctttctgaaattcccaacaatttacttc-tagaaagAAGACCTCAAATGTGCGGTGTCATGTCTTCGGGACAATAAACAAGTTTCCACTATAGGCCTTTGGGGGCGATCAATGGGTGCCGTTACATG
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagctacccctttttgcatgtatttatttctttaatcagtttccacaattgcatcttttatgcatctaactaaagtttctgtatgaaattaacgatgcagcacatctataaagttgcatgcttttttgtgtaattttcctgcaatgtttctcaagtttaatgtttcctgtgacagAAAGATGATCTCAAGATGGTGGTGTCACATTTAAGAAGCAACAAACAAGTATCTCGTATAGGACTTTGGGGACGATCAATGGGTGCTGTTACAAG
| | ||| || | || | || || || | | | | || ||| || || || | | | |||| ||||||||||||| ||||| || | | |||| || ||| |||||||| ||||| ||||||||||||||||| |||||||| ||||| ||
---------------------------------------------------------------------------------------------gtgtgttttcgggtct-tactttctcaaggttcttcgtcttttccttatctaaattttttcttcttaaa-----cttaagctagAAGGATGATCTCAAGACTGTGGTATCTTACCTGAGAAACAGCAATCAAGTATCCCGTATTGGACTTTGGGGACGATCTATGGGTGCAGTTACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttttgtgtaattttcctgcaatgtttctcaagtttaatgtttcctgtgacagAAAGATGATCTCAAGATGGTGGTGTCACATTTAAGAAGCAACAAACAAGTATCTCGTATAGGACTTTGGGGACGATCAATGGGTGCTGTTACAAG
gtttaat putative branch site (score: 4)
tgtttcct CT-rich tract
tttaatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctacccctttttgcatgtatttatttctttaatcagtttccacaattgcatcttttatgcatctaactaaagtttctgtatgaaattaacgatgcagcacatctataaagttgcatgcttttttgtgtaattttcctgcaatgtttctcaagtttaatgtttcctgtgacagAAAGATGATCTCAAGATGGTGGTGTCACATTTAAGAAGCAACAAACAAGTATCTCGTATAGGACTTTGGGGACGATCAATGGGTGCTGTTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT