Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgtttatgtgctttgctttttgagtgatttgtgtttgtgtaattttcattttgttgaatgtctgcctttttgttttgcagTGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAG
Basic information
species | Glycine max |
transcript | GLYMA01G27250.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G27250.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------gtaagttgtttatgtgctttgcttt---ttgag------tgatttgtgtttgtgtaattttcattttgt--tgaatgtctgcctttttgttt--tgcagTGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAG
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gtttggtttattatctttcccaccaatgtttttatgttgattctgtgttaaaatcttttactcacaatcagatgttttctctctcgaatttgggttaaggcatcatgattaatgagtgctggttccatactttgtgcttaaagccggattttgtttttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
upper sequence: GLYMA01G27250.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 3'ss of exon 2
------------------------gtaagttgtttatgtgctttgctttttgagtgatttgtgt---------ttgtgtaattttc-attttgttg-aatgtctgcct---ttttgttttgcagTGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAG
| | | |||| |||| ||| | | ||||| | | | | || | || |||||| | | || || |||||||| ||||||||| |||||||| || |||||||| ||||||||||| || || ||||| |||||||| ||||||| || |||||||| |
gtgagaaaaatcccccttgttactattatctaactatgagcttcccttgatcattgattcatttggcataggatcttatattcttagattttgatatggggcctttctatgttttgtttctcagTGATGGAAAGCTTGATATAGTGGTTCCTTCTTTTGTTCATTATCTGGAGGTCTTAGAAGGTTCTGATGGAGATAAAATGCCTG
upper sequence: GLYMA01G27250.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ25263 (Selaginella moellendorffii), 3'ss of exon 2
gtaagttgtttatgtgctttgctttttgagtgatttgtgtttgtgtaattttcattttgttgaatgtctgcctttttgttttgca-gTGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAG
||||| || ||||| | | | || || || | || || | | | || | |||||||| || || ||||| || |||||||| ||||||||||| || ||||| ||||| || ||||| || ||||||| ||
-------------------------gtgagt-atccttgtttctttc-tcttgatgcgaagaaaaatgtggattgatttgatacaagGGATGGGAAACTGGACATTGTTGTGCCGTCTTTCGTTCACTACCTCGATGTTCTTGAAGGAGCAGATGGTGAAAAAATGCAAG
upper sequence: GLYMA01G27250.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ23254 (Selaginella moellendorffii), 3'ss of exon 2
gtaagttgtttatgtgctttgctttttgagtgatttgtgtttgtgtaattttcattttgttgaatgtctgcctttttgttttgca-gTGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAG
||||| || ||||| | | | || || || | || || | | | || | |||||||| || || ||||| || |||||||| ||||||||||| || ||||| ||||| || |||||||| ||||||| ||
-------------------------gtgagt-atccttgtttctttc-tcttgatgcgaagaaaactgtggattgatttgatacaagGGATGGGAAACTGGACATTGTTGTGCCGTCTTTCGTTCACTACCTCGATGTTCTTGAAGGAGCAGATGGGGAAAAAATGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttgtgtttgtgtaattttcattttgttgaatgtctgcctttttgttttgcagTGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAG
tctgcctttttgtttt CT-rich tract
taattttcattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgtttatgtgctttgctttttgagtgatttgtgtttgtgtaattttcattttgttgaatgtctgcctttttgttttgcagTGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT