Sequence
atgc intronic sequence ATGC exonic sequencegtatggtattggccaggtactaattgttgcttttgttttgacgtcattgcaatcttttataggtcactagattttcgagtttcttacatttttttctacattgcttttagAGAGACAAACGAACTGGTACTCCTAAGGTATGGCTGTACCGGGATAAAGAAACTGATGAGCCCAAGGGAGATGCTACTGTTACCTATGAGGATCCGCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G50300.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 1
gtatggtattggccaggtactaattgttgcttttgttttgacgtcattgcaatcttttataggtcactagattttcgagtttcttacatttttt-tctacattgcttttagAGAGACAAACGAACTGGTACTCCTAAGGTATGGCTGTACCGGGATAAAGAAACTGATGAGCCCAAGGGAGATGCTACTGTTACCTATGAGGATCCGCATG
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-----ctctccatttaatattgtttcttgtcttttttttctcctctatgttgcatttttt----ttctaaactgttagtcctatttcctttgcaattcacatt--ttgcagAAAGATAAACGTACAGGGAGACCAAAAATATGGTTATATCGAGACAAAGAAACTAATGAACCAAAAGGAGATGCTACTGTAACATATGAGGATCCGCATG
upper sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G11060.1 (Glycine max), 3'ss of exon 1
--gtatggtattggccaggtactaattgttgcttttgttttgacgtcattgcaatcttttataggtcactagattttcgagtttcttacatttttttctacattgcttttagAGAGACAAACGAACTGGTACTCCTAAGGTATGGCTGTACCGGGATAAAGAAACTGATGAGCCCAAGGGAGATGCTACTGTTACCTATGAGGATCCGCATG
||| ||||| | | | || |||| || | ||||| |||||| ||| | | | || || | ||| | ||| | ||| ||| ||||| || || | || || ||||| | || || || ||||||||| |||| || || ||||||||||| || || ||||||||||||||||
ccatataatattgtt----tcttgtcttttttttttaccttctctatgttgca---ttttat----ttctaaactgttagtcttatttcctttgcaatt-catacttcgcagAAAGATAAACGTACAGGGAGACCAAAAATATGGTTATATCGAGACAAAGAAACTAATGAACCAAAAGGAGATGCTACCGTAACATATGAGGATCCGCATG
upper sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 1
-----------gtatggtattggccaggtactaattgttgcttttgttttg-acgtcatt------gcaatcttttataggtcactagattttcgagtttcttacatttttttct------acattgcttt-tagAGAGACAAACGAACTGGTACTCCTAAGGTATGGCTGTACCGGGATAAAGAAACTGATGAGCCCAAGGGAGATGCTACTGTTACCTATGAGGATCCGCATG
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gtagttaatctgactggctattatttgaaattccatattgtgcttgttttacaagccttttgttttgtaaaacttgataagttcaaatgctcatccttttcttccattttctttctcattcacgttcctttgtagAAAGACAAAAGAACAGGTCGACCTAAGATATGGTTGTACCGGGACAAAGTCACTAATGAACCAAAGGGTGATGCAACTGTAACATATGAGGATCCACATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttataggtcactagattttcgagtttcttacatttttttctacattgcttttagAGAGACAAACGAACTGGTACTCCTAAGGTATGGCTGTACCGGGATAAAGAAACTGATGAGCCCAAGGGAGATGCTACTGTTACCTATGAGGATCCGCATG
ttcttac putative branch site (score: 2)
tttttttctacatt CT-rich tract
tttcttacattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggtattggccaggtactaattgttgcttttgttttgacgtcattgcaatcttttataggtcactagattttcgagtttcttacatttttttctacattgcttttagAGAGACAAACGAACTGGTACTCCTAAGGTATGGCTGTACCGGGATAAAGAAACTGATGAGCCCAAGGGAGATGCTACTGTTACCTATGAGGATCCGCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT