Sequence
atgc intronic sequence ATGC exonic sequencegtataattgggttggatgcttgtatgtcccaataaaaaaaatggatttgctgtttgcttgctcgctattcctgtttcttcaacttgtgtttctcaacttgctattgtgtcttttttttgtcattcagatgaactagttatgttgcagcagtgttatgatacatccctgttgttggtatgtatgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCAAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
Basic information
species | Glycine max |
transcript | GLYMA13G40080.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g74460.2 (Oryza sativa), 3'ss of exon 5
gtataattgggttggatgcttgtatgtcccaataaaaaaaatggatttgctgtttgcttgctcgctattcctgtttcttcaacttgtgtttctcaacttgctattgtgt-cttttttttgtcattcagatgaactagttatgttgcagcagtgttatgatacatccctgttgttggtatgtatgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCAAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
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-------------------------------------------------------------gtgcttcccctgctgcattcatcc---taacacaattaatttctgtgggcttttggttgtgatt-acacaaacttactttctaaagttctcatccagatttctctatctgaaaatttaatttgtagATGCTGCTGATTTTGACCAAGTCTGTCAACAGATGCTTTGAGAAGAACCCTAAATTTGATATGGCACCATTGCTAGGTGGCACAGATGCAGTTTTCCTAT
upper sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G28390.1 (Arabidopsis thaliana), 3'ss of exon 5
gtataattgggttggatgcttgtatgtcccaataaaaaaaatggatttgctgtttgcttgctcgctattcctgtttcttcaacttgtgtttctcaacttgctattgtgtcttttttttgtcattcagatgaactagttatgttgcagcagtgtta-tgatacatccctgttgttggtatgtatgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCAAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
|| | |||| | ||| | ||| | | | | || | ||| || ||| || | | | | | | ||||| ||||||||||| | || ||||||| ||| || ||||||||||||| |||||| ||||||| |||||||||||||||||||| || ||||| ||||||||| |
-------------------------------------------------------------------------------------gtaaaaaatagtctgctgctctgtatcctttcttt--gtaacattttcatgtttgagtg-agcggtttaaataaccaaaatgcaatattggtg---atgcagATGATACTAATTTTAACAAAATCAATAGACAGATGTTTTGAAAAGAATGCAAAGTTCGATATGACACCCTTGCTTGGAGGGACAGATGCTGTCTTCTCAT
upper sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 5
gtataattgggttggatgcttgtatgtcccaataaaaaaaatggatttgctgtttgcttgctcgctattcctgtttcttcaacttgtgtttctcaacttgctattgtgtcttttttttgtcattcagatgaactagttatgttgcagcagtgttatgatacatccctgttgttggtatgtatgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCAAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
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-------------------------------------------------------------------------------------ctgcttaccgcttaagcattctgcccaattctgttttaacaaaaatattttttg-atatttatggtagttctccattcttttgattttgatatggatgcagATGCTACTTATTCTGACAAAGTCAGTAAATAGATGTTTTGAGAAGAATCCAAAGTTTGATATGACCCCTTTGCTCGGAGGAACAGATGTTGTCTTCTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actagttatgttgcagcagtgttatgatacatccctgttgttggtatgtatgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCAAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
ttatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataattgggttggatgcttgtatgtcccaataaaaaaaatggatttgctgtttgcttgctcgctattcctgtttcttcaacttgtgtttctcaacttgctattgtgtcttttttttgtcattcagatgaactagttatgttgcagcagtgttatgatacatccctgttgttggtatgtatgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCAAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA