Sequence
atgc intronic sequence ATGC exonic sequence...ctcgatatagagacctaccttttaagtaacatttttgaataaggtacccagttaattccatccagtaccattgtaataactttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGACATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGGGATCTTGCTGTTTTCT
Basic information
species | Glycine max |
transcript | GLYMA04G24430.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G318635_T01 (Zea mays), 3'ss of exon 17
ctcgatatagagacctaccttttaagtaacatttttg---aataaggta--cccagttaattccatccagtaccattgtaataactttagctgtggttttgc-tagGCAACTATCTATCAGCAAAAGGCACTAGACATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGGGATCTTGCTGTTTTCT
||| || | | | ||| ||||| || | ||| | | || | | || | | |||| | | |||| ||| ||||||| |||||||| || ||||| |||| |||||||| || || |||||||| ||||| || ||||| |||||||| ||||| ||||||||||||||||
------atatgcacttgtcaggtgtttaatttttttccacaacagcgtagttctatcctatgctgtgaaggcttaactttataaatgttgctgctctttcaaacagGCAACCATCTATCAACAGAAGGCTTTAGATATTAATGAGAGGGAACTTGGACTTGACCACCCAGATACAATGAAAAGCTATGGAGATCTTGCTGTTTTCT
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv11s0037g00840.t01 (Vitis vinifera), 3'ss of exon 17
--ctcgatatagagacctaccttttaagtaacatttttgaataaggtacccagttaattccatccagtaccattgtaataactttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGACATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGGGATCTTGCTGTTTTCT
|| || | ||| || || | ||| | | | | || | | || ||| || | | || | | |||| |||||||| |||||||||||||| || | || || ||||| |||||||||||||| || ||||||||||| |||||||||||||||||||||||||||||||
cacttcatttgaagaaagacattgtcctgggattttctatttgaaaaataatattcacattaaattgtttcatattattggccctatttat--ttttcgtagGCAACCATCTATCAGCAAAAAGCTTTGGATATCAATGAGAGAGAGCTTGGACTTGATCATCCTGATACAATGAAAAGTTATGGGGATCTTGCTGTTTTCT
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
ctcgatatagagacctaccttttaagtaacatttttgaataaggtacccagttaattccatccagtaccattgtaataactttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGACATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGGGATCTTGCTGTTTTCT
| | | || ||||| || | || | || ||||| |||| | |||| | || || |||||||| || | ||||| ||||| || ||||||||||| |||||||| ||||| |||||||| ||||| || | ||||| || |
----------------------------gtacacaaaagctacatattgtattaatgtaattgatgacttaattgatgacttt--ttgtgatc-----agGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acccagttaattccatccagtaccattgtaataactttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGACATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGGGATCTTGCTGTTTTCT
taataac putative branch site (score: 1)
ttttgct putative PPT
attgtaataacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcgatatagagacctaccttttaagtaacatttttgaataaggtacccagttaattccatccagtaccattgtaataactttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGACATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGGGATCTTGCTGTTTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - -cctacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctgtg