Sequence
atgc intronic sequence ATGC exonic sequencegtgcttgagccatacatggatctctgtttgttatttcttgtttatgcttatgttctgatgttatttgtctttattcttgcttaagGTTTCTGTTTTTGACTCGGTCGTGCAAGGCGGTGACTCTGTATGGGAAGGTCTTCGTATATACAAAGGGAAAGTATTTAAGCTTGAAGAACATCTAGACC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G27410.2 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 8
---------------------------gtgcttgagccatacatggatctctgtttgttatttcttgtttatgcttatgttctgatgttatttgtctttattcttgcttaagGTTTCTGTTTTTGACTCGGTCGTGCAAGGCGGTGACTCTGTATGGGAAGGTCTTCGTATATACAAAGGGAAAGTATTTAAGCTTGAAGAACATCTAGACC
| || | | | || | | | || | || | || || ||| | ||| ||||| || | ||| | |||||||||| ||||| || || || ||||| |||||||| || |||||||| ||||| |||| || || || ||||||||||||| || |||||||||
gtaattaattgtatgacacttaaaattcttctgtatgctttgatataacaaagcttcagagttat-acagattctcatggtttgaaattattaccctgtgatctatc---agGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTATATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA
upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA10G29770.1 (Glycine max), 3'ss of exon 9
gtgcttgagccatacatggatctctgtttgttatttcttgtttatgcttatgttctgatgttatttgtctttattcttgcttaagGTTTCTGTTTTTGACTCGGTCGTGCAAGGCGGTGACTCTGTATGGGAAGGTCTTCGTATATACAAAGGGAAAGTATTTAAGCTTGAAGAACATCTAGACC-
| | |||||||||| ||||| || || || ||||| |||||||| || ||||| |||||||| | || || || || ||||||||||||| ||||||||||||
------------------------------------------------------------------------------gtatcaggtttctgtgtttgattcagttgtccaaggaggtgactcagtttgggagGGTCTTCGAGTGTATAATGGAAAGATATTTAAGCTTGAGGAACATCTAGACAG
upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA19G42530.1 (Glycine max), 3'ss of exon 8
---------------------------gtgct-tgagccatacatggatctctgtttgttatttcttgtttatgcttatgttctgatgttatttgtctttattcttgcttaagGTTTCTGTTTTTGACTCGGTCGTGCAAGGCGGTGACTCTGTATGGGAAGGTCTTCGTATATACAAAGGGAAAGTATTTAAGCTTGAAGAACATCTAGACC
|||| | || | || || | | || | || | || || ||| | ||| ||||| || | ||| | |||||||||| ||||| || || || ||||| |||||||| || |||||||| ||||| | || || || || ||||||||||||| || |||||||||
gtgattaattgtatgacacttaaaagtctgctgtatgctgttgatagagcaaagcttcagagttat-acagattctcatggtttgaaattattaccctgtgatctatc---agGTTTCTGTGTTTGATTCAGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTGTATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA
upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 18
---------------gtgcttg---agccatacatggatctctgtttgttatttcttgtttatgcttatgtt-ctgatgttatttgtctttattcttgcttaagGTTTCTGTTTTTGACTCGGTCGTGCAAGGCGGTGACTCTGTATGGGAAGGTCTTCGTATATACAAAGGGAAAGTATTTAAGCTTGAAGAACATCTAGACC
| ||| | | | | | | | | | ||| | | | ||||||| |||||| || | | | | || |||||||||| || |||||||| || || ||||| ||||| || || ||||| || ||||| || ||||| ||||| |||||||||||||||| ||| ||||
gtactcttatattggatatttggagaatcttcctggaaaattttaacatcattgagctctca-gtttatgtttctgatgc-ataattttgtgattttttttaagGTTTCGGTGTTTGACTCTGTTGTCCAAGGTGGTGATTCAGTGTGGGAGGGGCTTCGAATTTACAACGGGAAGATATTTAAGCTTGAAGAGCATTTAGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttcttgtttatgcttatgttctgatgttatttgtctttattcttgcttaagGTTTCTGTTTTTGACTCGGTCGTGCAAGGCGGTGACTCTGTATGGGAAGGTCTTCGTATATACAAAGGGAAAGTATTTAAGCTTGAAGAACATCTAGACC
ttctgat putative branch site (score: 3)
tttgtctttattctt putative PPT
ttatttgtctttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttgagccatacatggatctctgtttgttatttcttgtttatgcttatgttctgatgttatttgtctttattcttgcttaagGTTTCTGTTTTTGACTCGGTCGTGCAAGGCGGTGACTCTGTATGGGAAGGTCTTCGTATATACAAAGGGAAAGTATTTAAGCTTGAAGAACATCTAGACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC