Sequence
atgc intronic sequence ATGC exonic sequencegtactatcttgaagacgttgatgaaacctagttttgtttgtgatatgagtctaaagtcttagtcttatgaatatatctctgtttctctatatatgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTACGATGGACAAACTATTTGAGACCAGACATTAAGCGAGGAAAATTCTCTGCGGAGGAAGAAGAGACCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65230.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g51799.1 (Oryza sativa), 3'ss of exon 1
------gtac-tatcttgaagacgttg-atgaaacctag-ttttgtttgtgatatgagtctaaa----gtcttagtcttatgaatata---------tctctgtttctctatatat-gcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTACGATGGACAAACTATTTGAGACCAGACATTAAGCGAGGAAAATTCTCTGCGGAGGAAGAAGAGACCAT
|||| | || | | | | | | | | | |||| | || || ||| | ||| ||| || | || ||| | || || | ||||| || ||||||||||| ||||| ||||||||| ||||||| ||||| |||| |||||||| ||| ||||||| ||| | | | || | || |||||
gtatgtgtacatgcacaacggatggcgtacgtagctttgatcttgtagctagcatcgatccaaatgcagctatagctcgatggccatggcgttgagttttccttttttttacatgttgcagGGCTGAACAGGTGTGGCAAGAGCTGCAGGCTAAGATGGACGAACTACCTGAGGCCAGACATCAAGAGAGGAAAGTTCACCTCTGCCGAGAAGGATACCAT
upper sequence: AT5G65230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G159547_T01 (Zea mays), 3'ss of exon 1
---------------gtactatcttgaagacgttgatgaaacctagttttgtt-tgtgatatgagtctaaagtcttagtcttatgaatatatctc---tgtttctctatatatgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTACGATGGACAAACTATTTGAGACCAGACATTAAGCGAGGAAAATTCTCTGCGGAGGAAGAAGAGACCAT
| || | | | | | | | || | ||| | | ||| | | | | | ||| || ||| | | | | |||||| || ||||||||||| ||||| |||||||| ||||||| ||||| ||||| |||||||| ||| |||| || ||| | |||||||||| |||||||
gtacgtgactgccgggaacaaacctctccatttctctcggtctcggtgtgacgatgtaaaagaggtcgatcgcttccatgcga-aaatgtagctcatcgatctagttgttattgcagGGCTCAACAGGTGTGGCAAGAGCTGCAGGCTGAGATGGACCAACTACTTGAGGCCAGACATCAAGAGAGGGAAGTTCACCCAGGAGGAAGAACAGACCAT
upper sequence: AT5G65230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv11s0078g00480.t01 (Vitis vinifera), 3'ss of exon 1
-----------gtact--atcttgaagacgttgatgaaacctagttttgtttgtga-----tatgagtctaaagtcttagtcttatgaatatatctctgtttctctatatatgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTACGATGGACAAACTATTTGAGACCAGACATTAAGCGAGGAAAATTCTCTGCGGAGGAAGAAGAGACCAT
| | ||||| || | ||| || | ||| || ||| |||| || || | ||| | | | ||| ||| || | |||||||||| || ||||||||||||||||| || ||||||| || |||||||| || || || ||| |||| ||||| ||| || ||||| ||||| ||
gtacaattcacacaatgaatcttttttttttttttttttcctttttctttttttgggtatctatctgtctctagcaaaaggc--atgggtgttcttaattttgtcttaatttacagGTCTTAATAGATGTGGGAAGAGTTGCAGATTAAGATGGACTAATTATTTGAGGCCTGATATCAAGAGAGGGAAATTTTCTCGAGAAGAAGAGGAGACAAT
upper sequence: AT5G65230.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0141g00100.t01 (Vitis vinifera), 3'ss of exon 1
gtactatcttgaagacgttgatgaaacctagttttgtttgtgatatgagtctaaagtc--ttagtcttatgaatatatctctgtttctctatatatgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTACGATGGACAAACTATTTGAGACCAGACATTAAGCGAGGAAAATTCTCTGCGGAGGAAGAAGAGACCAT
|||| || | || ||| || |||| ||| | ||| ||| | ||| | | | ||| ||||||| | |||||||||| || ||||||||||||||||| || ||||||| || |||||||| || || || ||| |||| ||||| ||| || ||||| ||||| ||
gtacaattc---acacaatgaatcccccctttttttttttgggtatctatctgtcactagcaaaaggcatgggtgttcttaattttgtctatatttacagGTCTTAATAGATGTGGGAAGAGTTGCAGATTAAGATGGACTAATTATTTGAGGCCTGATATCAAGAGAGGGAAATTTTCTCGAGAAGAAGAGGAGACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgagtctaaagtcttagtcttatgaatatatctctgtttctctatatatgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTACGATGGACAAACTATTTGAGACCAGACATTAAGCGAGGAAAATTCTCTGCGGAGGAAGAAGAGACCAT
gtctaaa putative branch site (score: 3)
tctctgtttctctat putative PPT
tcttatgaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactatcttgaagacgttgatgaaacctagttttgtttgtgatatgagtctaaagtcttagtcttatgaatatatctctgtttctctatatatgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTACGATGGACAAACTATTTGAGACCAGACATTAAGCGAGGAAAATTCTCTGCGGAGGAAGAAGAGACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA