Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcattaaattatcatatccattattcactttatttttctgtgaaaagcagatttgttactttgctttttcttccgtcagGAATTGGTTATAATGGGTTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCACAG
Basic information
species | Glycine max |
transcript | GLYMA17G13950.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G13950.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 3
---------------gtaagttcattaaattatcatatccattattcactttatttttct-gtgaaaagcagatttgttactttgctttttcttccgtcagGAATTGGTTATAATGGGTTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCACAG
||| ||| || || || || ||| | ||| | | | || | ||| || | || | | |||||||| || |||||||| ||||| |||||||||||||| | ||||||||||||||| ||
gcattgctgtgaaatgtatgttgttttggcaggca-atgcaccattaataatatgtatatcatgttgttctgatagtgtaacccaatcttaatgcaatcagGAATAGGGTATAATGGATTTCCTAGAGGTTGTTCTGACAATAAGCTACCCTGGGCAAAG
upper sequence: GLYMA17G13950.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G124091_T04 (Zea mays), 3'ss of exon 3
---------gtaagttcatta-aattatcatatccattattcactttatttttctgtgaaaagcagatttgt-----tactttgctttttcttccgtcagGAATTGGTTATAATGGGTTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCACAG
| | |||| || | ||| | | || | ||| || | | |||| || | || || | |||||||||| || ||||| || || ||||||||||| ||||||||||| || |||||| ||
ttttctgtgatgggcccattgtgatgaatatagctgtcatgttcaacttttaaagctgcatattgtctttgacaacgtaactcagttgttttctaaccagGAATTGGCTACAATGGCTTCCCTAGAGGTTGTTCCGATGACAAGCTTCCTTGGGCAAAG
upper sequence: GLYMA17G13950.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G48540.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------gtaagttcattaaattatcatatccattat-tcactttatttttctgtgaaaagcagatttg---------ttactttgctttttcttccgtc-agGAATTGGTTATAATGGGTTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCACAG
| | | || || | | |||| | |||||| | | || | || || | | | || |||| | | ||| ||||| |||||||| ||||||||||| || ||||||||||| || || ||||| ||
gtaagataatacgatcacacttgtgttttgatctctttgaacaacatgaagtgtggttgtatagtttatttcattttgtcacttagctggtacatgcgagacacatataaacgaggactcaaaaactttcatctttcatttagGGATTGGCTATAATGGTTTTCCAAGAGGCTGCTCTGATGACAAACTTCCTTGGGCCAAG
upper sequence: GLYMA17G13950.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g01370.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtaagt-tcatt-aaattatcatatccatt-attcactttatttttctgtgaaaagcagatttgttactttgctttttcttccg-tcagGAATTGGTTATAATGGGTTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCACAG
| || ||||| | ||| | || | | || | | | || || | | | | | || | | | ||||| ||||| ||||||||||| |||||||| ||||| ||||||||||| || |||||| ||
gatcatagttactgagcatcattcagattgtaatgtgctttgagtttgatcgccgttatgatagttcttacaccatcattcggattctcttcttggtcagGCATTGGCTATAATGGGTTCCCAAGAGGCTGTTCAGATGACAAGCTCCCTTGGGCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcactttatttttctgtgaaaagcagatttgttactttgctttttcttccgtcagGAATTGGTTATAATGGGTTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCACAG
tttgttactttgcttt CT-rich tract
ttatttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcattaaattatcatatccattattcactttatttttctgtgaaaagcagatttgttactttgctttttcttccgtcagGAATTGGTTATAATGGGTTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT