Sequence
atgc intronic sequence ATGC exonic sequence...gcttttcagtttgcatagatctagatgtttcttgtgtttttcctaaactttagagttagcgtgtgttgtgaagtgagagtgatgtgatttgtgattgcagTTGCCAAGCATTGACATAAATCCGCAGTTCATCACTTTCACGCATGTGACGATGGAGTCTGATAAGTATATATGCGTTCGAGAAACGGCTCCGCAGAATA
Basic information
species | Glycine max |
transcript | GLYMA15G25450.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G25450.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 1
gcttttcagtt--tgcatagatctagatgtttcttgtgtttttcctaaactttagagttagcgtgtgttgtgaagtgagagtgatgtgatttgtga---ttgcagTTGCCAAGCATTGACATAAATCCGCAGTTCATCACTTTCACGCATGTGACGATGGAGTCTGATAAGTATATATGCGTTCGAGAAACGGCTCCGCAGAATA
||| |||| || | | | | || || | | || || ||||| | || || ||| | || |||| | || ||| | || ||| ||| || || ||||||||||| || || |||| || ||||||||||||||||| ||||| || ||||| ||||| |||||||| |
---tttaagttattgtgttgcgcaatgtgcttatctactcggatcttgtaacta-agttaatgaactatgccaattgattact-tttgttttggaaattttccagCTTCCGAGCGTTGGGATCGGTCAACAGTTCATCACCTTTACAAATGTTACTATGGAGTCTGATAAGTACATATGTGTACGAGAGACGGCACCGCAGAACA
upper sequence: GLYMA15G25450.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 1
-----gcttttcagtttgcatagatctagatgtttcttgtgtttttcctaaactttagagttagcgtgtgttgtgaagtgagagtgatgtgatttgtgattgcagTTGCCAAGCATTGACATAAATCCGCAGTTCATCACTTTCACGCATGTGACGATGGAGTCTGATAAGTATATATGCGTTCGAGAAACGGCTCCGCAGAATA
||| | ||| | | ||| | | | | | | | | | ||| | | | ||| | | |||| |||| || ||||||||||| || | | || | ||| ||||| || || || || ||||| |||||||| |||||||||||| |||||||||| || |||||||| ||||| |
tatgcgctgatggttttacgtg---ctaaaaatcttgcatttgtgttgtggtttggagaaatggaattgaatgttgggattgtttgatttgat--gtacttgcagTTGCCGAGTTTGGGAATTAGTCCTCAGTTTATAACGTTTACACATGTCACGATGGAATCTGATAAGTATCTATGCGTTCGGGAGACGGCTCCACAGAACA
upper sequence: GLYMA15G25450.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 1
-gcttttcagtttgcatagatctagatgtttcttgtgtttttcctaaactttagagttagcgtgtgttgtgaagtgagagtgatgtgatttgtgattgcagTTGCCAAGCATTGACATAAATCCGCAGTTCATCACTTTCACGCATGTGACGATGGAGTCTGATAAGTATATATGCGTTCGAGAAACGGCTCCGCAGAATA
|| | || || | | | || ||| | | | | | ||| || | | | | | | | | ||||| || | || ||| || || | ||| ||| | || ||||| ||||||||||||||||||||||| || || ||||| || || ||| | || || || |
agcgagaggcagggggaggagggagtgaaaacgtaagggttgggaaaatggcggtggttgag-gtgctgatggtttgggataacggggtggtgcaatgcagCTGACGAGTCTTGGGATTAACCAGCAATTCGTTACGTTCACACATGTGACGATGGAGTCTGATAAATACATTTGCGTACGGGAGACGTCGCCTCAAAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactttagagttagcgtgtgttgtgaagtgagagtgatgtgatttgtgattgcagTTGCCAAGCATTGACATAAATCCGCAGTTCATCACTTTCACGCATGTGACGATGGAGTCTGATAAGTATATATGCGTTCGAGAAACGGCTCCGCAGAATA
tcctaaa putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttttcagtttgcatagatctagatgtttcttgtgtttttcctaaactttagagttagcgtgtgttgtgaagtgagagtgatgtgatttgtgattgcagTTGCCAAGCATTGACATAAATCCGCAGTTCATCACTTTCACGCATGTGACGATGGAGTCTGATAAGTATATATGCGTTCGAGAAACGGCTCCGCAGAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - -tttgcat
- - - - - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtg