Sequence
atgc intronic sequence ATGC exonic sequencegtaatagtctctcagctcttatattttcctcactgatagacatgctatttgattatatctccatttttgacttattgttttgttgtttacctgagattataattgagtttgtgttgttggcttttggtgttgccttttttgcagACAGCTCAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTGGTTATGAAGCGTTCTCAACCTAAAGTACTGCGCTTGAATTTGATT
Basic information
species | Glycine max |
transcript | GLYMA07G01350.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G01350.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 4
gtaatagtctctcagctcttatattttcctcactgatagacatgctatttgattatatctccatttttgacttattgttttgttgtttacctgagattataattgagtttgtgttgt-tggcttttggtgttgcct-tttttgc-----agACAGCTCAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTGGTTATGAAGCGTTCTCAACCTAAAGTACTGCGCTTGAATTTGATT
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--------------------------------------------------------------gtaagggtcaaatcctattacagtgtgcataaatacatcataaccttttttttttctgttttcttatgtttcatgtttctgctaattagGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG
upper sequence: GLYMA07G01350.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G057618_T02 (Zea mays), 3'ss of exon 4
gtaatagtctctcagctcttatattttcctcactgatagacatgctatttgattata-tctccatttttgacttattgttttgttgtttacctgagattataattgagtttgtgttgttggcttttggtgttgccttttttgcagACAGCTCAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTGGTTATGAAGCGTTCTCAACCTAAAGTACTGCGCTTGAATTTGATT
||||| ||| | |||| | |||| | | || | | ||||| || | || |||| || || || |||| || ||| || | | | ||||| || ||| || || | | || || ||||| ||||| || |||| || || ||||| |||||||| ||||||||||||||||| |||||||| || || | ||| | |
gtaatggtc----aactctcaa---ctcctga--aacagtagttttttttgaatacagcctacattctttcattgttatttt--tgctta------------ataaattgtatgttgctg----------ctgcttt------agGGATTTGAAGCACGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGTTCTCAGCCTAAAGTCCTTCGGCTTAATCTTGTG
upper sequence: GLYMA07G01350.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G480607_T06 (Zea mays), 3'ss of exon 3
gtaatagtctctcagctcttatattttcctcactgatagacatgctatttgattatatc-tccatttttgacttattgttttgttgtttacctgagattataattgagtttgtgttgttggcttttggtgttgccttttttgcagACAGCTCAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTGGTTATGAAGCGTTCTCAACCTAAAGTACTGCGCTTGAATTTGATT
||| | || || | | | |||| || ||| | | || || || || |||| || ||| || | ||| ||||| || || || ||| ||| | | || |||||||| ||||| || |||| || || ||||| |||||||| ||||||||||| ||||| |||||||| || || | ||| | |
------------------gtatggtcaactgctaaatcagta-gtttcttgaatacatcctacgttctttcattgttatttt--tgctta------------ataaattttatgttgctg----ctgctgctgct-------cagGGATTTGAAGCATGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGATCTCAGCCTAAAGTCCTTCGACTTAATCTTGTG
upper sequence: GLYMA07G01350.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g02420.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------gtaatagtctctcagctcttatattttcctcactgatagacatgctatttgattatatctccatttttgacttattgttttgttgtttacctgagattataattgagtttgtgttg--ttggcttttggtg--ttgccttttttgcagACAGCTCAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTGGTTATGAAGCGTTCTCAACCTAAAGTACTGCGCTTGAATTTGATT
| || | | | | || | ||||| ||| | ||||| | | | || | | | ||| || ||| | | | || || || | || |||| | || ||| || | ||||| |||||||||||||||||||| | |||||||| || ||||| || |||||||||||||||||||| || ||||||||||| || |||||||||||| ||
gtaatatactctttctaatttttccataaaaatgtttttatttatttatttattttcatttccctcctgggaattcctttatttctctgtcaagctgttgtctattaatttcttggttcagcagttatgtccttattttcattactcttcccttggttaaaagttacttgtgttatgtgcagGCAGCTCAAACATGAGGAAAAATGCTGCATGGAGGAGCTGCAATGCAACATTGTGGTTATGAAGCGCTCCCAACCTAAAGTTCTCCGCTTGAATTTGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgagattataattgagtttgtgttgttggcttttggtgttgccttttttgcagACAGCTCAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTGGTTATGAAGCGTTCTCAACCTAAAGTACTGCGCTTGAATTTGATT
ttgcctttttt CT-rich tract
attataattgagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagtctctcagctcttatattttcctcactgatagacatgctatttgattatatctccatttttgacttattgttttgttgtttacctgagattataattgagtttgtgttgttggcttttggtgttgccttttttgcagACAGCTCAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTGGTTATGAAGCGTTCTCAACCTAAAGTACTGCGCTTGAATTTGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC