Sequence
atgc intronic sequence ATGC exonic sequence...ggaggtgatttgttttagctgttgtgtttccaaggttaaaagcataaggtcagtattttgagaaacatttctccttaatgtgatactgtgcaatttgtagGCACTTACTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTG
Basic information
species | Glycine max |
transcript | GLYMA11G19930.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G19930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 2
ggaggtgatttgttttagctg-ttgtgtttccaaggttaaaagcataaggtcagtattttgagaaac-atttctccttaatgtgatactgtgcaatttgt---agGCACTTACTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTG
|||| | | ||| | | | | || ||| | |||||| | | |||| || || | || |||| || | || | |||| ||| ||||||||||||| ||||| || | || || ||||||||||| || || || ||| | |||||| ||||||||||||||||||| | ||
-----caatttttcatcactgatcttatctgtcagaataactgaataaggctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTG
upper sequence: GLYMA11G19930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G165195_T02 (Zea mays), 3'ss of exon 2
ggaggtgatttgttttagctgttgtgtttccaaggttaaaagcataaggtcagtattttga-gaaacatttctccttaatgtgatactgtgcaatttgt---agGCACTTACTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTG---
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----------------actgatcttatctgtcagaataactgaataaggctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatgacaggctcttgctaagGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCG
upper sequence: GLYMA11G19930.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 3
ggaggtgatttgttttagctgttgtgtttccaaggttaaaagcataaggtcagtattttgagaaacatttctccttaatgtgatact--gtgcaatttgtagGCACTTACTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTG
| | | || | || | | ||| || | | | | | |||| | ||| ||||| | | | | ||||| || ||||| ||| |||| ||||||||||||| | ||| |||||||||||| ||||||| || || ||| ||||||| ||||||||||||||||| || ||||
tcaaatcaattctcttgtggaccagttagttatagttttaa-cttgaaattatccttttttccc-tttccctctttaattttcttcctcataaaattttcagACACTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggtcagtattttgagaaacatttctccttaatgtgatactgtgcaatttgtagGCACTTACTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTG
ccttaat putative branch site (score: 4)
agtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaggtgatttgttttagctgttgtgtttccaaggttaaaagcataaggtcagtattttgagaaacatttctccttaatgtgatactgtgcaatttgtagGCACTTACTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
ggaggtg
- - - - - - - - -gctgttg
- - - - - - - - - - - - tgtttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatactg