Sequence
atgc intronic sequence ATGC exonic sequence...ttattgcgacaatgtcatttttccctttcatttgggactttgaggggggggggggggggataatgtttcagcatattttattgttgtgacattaatgcagGTTGTTTATAATGCAAACAAACTTGCAAAGTTGGTTAAAAAGAAGAAGAAGTTGCAGAATTGGCTTGTATATTATCAAAACAAAGTTGAAAGAACTTCAG
Basic information
species | Glycine max |
transcript | GLYMA17G01400.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 5
-ttattgcgacaatgtcatttttccctttcatttgggactttgagggggggggggggggga-taatgtttcagcatattttattgttgtgacattaatgcagGTTGTTTATAATGCAAACAAACTTGCAAAGTTGGTTAAAAAGAAGAAGAAGTTGCAGAATTGGCTTGTATATTATCAAAACAAAGTTGAAAGAACTTCAG
| || || | || | | || || | || | || | | || || ||| | || | | | ||||||| ||||||||||| || |||| ||| |||| ||| |||||||||| ||||||||||||||| || ||||| ||| |||||||| | ||
ttagttttaactgcttatcgttactaaaaaaaaaaaatctatgctctgatatggcttaccactaccatgttcttatcattcatt-tcatgg-actggtatagGTTGTCTATAATGCAAATAAGCTTGATAAGATGGTCAAAGAGAAGAAGAAAATGCAGAATTGGCTTGATTACTATCAGCTGAAATATGAAAGAAATACAT
upper sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 5
-----ttattgcgacaatgtcattttt---ccctttcatttgggactttgaggggggggggggggggataatgtttcagcatattttattgttgtgacatta-atgcagGTTGTTTATAATGCAAACAAACTTGCAAAGTTGGTTAAAAAGAAGAAGAAGTTGCAGAATTGGCTTGTATATTATCA----AAACAAAGTTGAAAGAACTTCAG
|| | || | | | ||| || ||| ||| |||| | | || |||| | || | | | |||||| | | ||| ||||||| | ||||||||||| || || | ||||| ||||||||||| ||| ||||||||||||||| || || || ||| | | | || ||||
gcaagttccttagaagttttaaatttgaaaccgtttagtttt---ctttaaaattatgctcttcttga-gatgtaagaaca-acataaacattgtgagacgatatgtagGTTGTATGCAATGCAAACAAGCTGGCCGATTTGGTGAAAAAGAAGAAAAAGCTGCAGAATTGGCTTGATTACTACCAGCTCAAATACGCTAGGAATAACT----
upper sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 4
-ttattgcgacaatgtcatttttccctttcatttgggactttgaggggggggggggggggataatgtttcagcatattttattgttgtgacattaatgcagGTTGTTTATAATGCAAACAAACTTGCAAAGTTGGTTAAAAAGAAGAAGAAGTTGCAGAATTGGCTTGTATATTATCAAAACAAAGTTGAAAGAACTTCAG
|| || || ||| | | | | || | | || | || | | || | | || | || | || | || ||||||||||| ||| ||||||| ||||||||||| ||||| || |||||| | || ||||||||||||||| |||||||||| ||| | |||| | |
tttctttagaaaatctagtataaacattgaaatgggtaattcaaaatataaagcattaaaatgtttatattcaatttcctaat-ttagaagttttatgcagGTTGTATATGATGCAAATAAACTTGCAAAATTGGTCAAGAAGAAGGAAAAAATGCAGAATTGGCTTGACTATTATCAAATTAAATATTCTAGAAATGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggggggggggggggataatgtttcagcatattttattgttgtgacattaatgcagGTTGTTTATAATGCAAACAAACTTGCAAAGTTGGTTAAAAAGAAGAAGAAGTTGCAGAATTGGCTTGTATATTATCAAAACAAAGTTGAAAGAACTTCAG
cattaat putative branch site (score: 3)
atattttattgttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattgcgacaatgtcatttttccctttcatttgggactttgaggggggggggggggggataatgtttcagcatattttattgttgtgacattaatgcagGTTGTTTATAATGCAAACAAACTTGCAAAGTTGGTTAAAAAGAAGAAGAAGTTGCAGAATTGGCTTGTATATTATCAAAACAAAGTTGAAAGAACTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - -caatgtc
- - - - - - - - - - - ccctttc
- - - - - - - - - - - - - - - - - -gactttg
- - - - - - - - - - - - - - - - - - - - - -ggggggg