Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcccttttgacatgaacttttctacacactctgagatgtgagggattctttgaatctcgtagtctaatgttcagcttcactggatcttgatatatgcagGATTCTTCTGGTATTTTCTGGGATAACGATAGCTTAGCTGCTCTACTGGCGTTGGAACTGAAAGCTGATCTTCTGATTCTTCTGAGCGATGTTGAAGGTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39800.4 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39800.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g38150.2 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------gtttgtcccttttgacatga-acttttctacacactctgaga----tgtgagggattctttgaatc-tcgtagtctaatgttcagcttcactggatcttgatatatgcagGATTCTTCTGGTATTTTCTGGGATAACGATAGCTTAGCTGCTCTACTGGCGTTGGAACTGAAAGCTGATCTTCTGATTCTTCTGAGCGATGTTGAAGGTC
| | | | | ||| || ||| | | | | | || ||| || | | | ||| | | | | || |||| || | || |||||||| |||||||| ||||||||||| || || ||||| | || |||| ||||||||||||||||||| || ||||| || || ||||| || ||
gtatgtaagtgtgtttcataccatacatctcctggaaaagtatgaaacttcagtttttgcgtggtgctgctctttagctgctacttattgttatactgcttgtatgcctagccctagggccttgtcagtgtatatgcaaatagccatgactttctaaccacactcacctataattctttta--cagGATTCATCTGGTATATTCTGGGATAATGACAGTTTAGCAGGACTGTTGGCACTGGAACTGAAAGCTGATCTCCTTATTCTGCTCAGTGATGTGGATGGGT
upper sequence: AT2G39800.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G41850.1 (Glycine max), 3'ss of exon 2
gtttgtcccttttgacatgaacttttctacacactctgagatgtgagggattctttg-aatctcgta-gtctaa---tgttcagcttcactggatcttgatatatgcagGATTCTTCTGGTATTTTCTGGGATAACGATAGCTTAGCTGCTCTACTGGCGTTGGAACTGAAAGCTGATCTTCTGATTCTTCTGAGCGATGTTGAAGGTC
|| || || |||| ||| | | ||| | || | ||||||| | | || | ||| | || ||| | || | | ||||||||||||||||||| || |||||||| ||||| ||| ||||||| |||| ||||| | ||||| |||||||| || | |||| ||||| |||||||
--ttttcttttccagattgaaagttt------agtttgaagt-tgctgcattctttccagttctatatatttaagtacatcaagtgtcattaacgttttttttgtgcagGATTCTTCTGGTATATTTTGGGATAATGATAGTTTATCTGCTCTGTTGGCCTTGGAGTTAAAAGCCGATCTTCTTGTTTTGTTGAGTGATGTAGAAGGTC
upper sequence: AT2G39800.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 2
gtttgtcccttttgacatgaacttttctacacactctgagatgtgagggattc-tttgaatctcgtagtctaatgttcagcttcactggatcttgatatatgcagGATTCTTCTGGTATTTTCTGGGATAACGATAGCTTAGCTGCTCTACTGGCGTTGGAACTGAAAGCTGATCTTCTGATTCTTCTGAGCGATGTTGAAGGTC
| ||| |||| || || | ||| | | | | | | ||| |||| | || | || ||| | | ||| ||||||||||||||||||| || |||||||| ||||| ||| ||||||| |||| ||||| | ||||| |||||||| || | |||| ||||| |||||||
gaatgtttagtttggaattg-ctacctggaatactt---gctttattgtttccatttctatctattcaagta-catcaagtgtcattaacgtattttatgtgcagGATTCTTCTGGTATATTTTGGGATAATGATAGTTTATCTGCTCTGTTGGCCTTGGAGTTAAAAGCCGATCTTCTTGTTTTGTTGAGTGATGTAGAAGGTC
upper sequence: AT2G39800.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------gtttgtcccttttgac-atgaacttttctacacactctgagatgtgagggattctttgaatctcgtagtctaatgttcagcttcactggatcttgatatatgcagGATTCTTCTGGTATTTTCTGGGATAACGATAGCTTAGCTGCTCTACTGGCGTTGGAACTGAAAGCTGATCTTCTGATTCTTCTGAGCGATGTTGAAGGTC
| | | ||| | ||| || ||| || | | | | |||| | || | || | || || | | || ||||| ||| | | |||||||||||||||||| || || |||||||| || || ||| | ||| || |||| |||||| | |||||||||||||| ||| | |||| ||||| || ||||
gtttgttattctacttgtctggtttgttatcagagcagaacttaatcttagagctgattgcttcaagctatgcacctttataaaaaaaaaaacaggtgacgtatgagactagactag-agaatact-taaagtgtcactaaatcat--tttatgcagGATTCTTCTGGCATATTTTGGGATAATGACAGTTTATCAGCTTTATTGGCATTGGAATTAAAAGCTGATCTTCTTATTTTGTTGAGTGATGTAGAGGGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctttgaatctcgtagtctaatgttcagcttcactggatcttgatatatgcagGATTCTTCTGGTATTTTCTGGGATAACGATAGCTTAGCTGCTCTACTGGCGTTGGAACTGAAAGCTGATCTTCTGATTCTTCTGAGCGATGTTGAAGGTC
ttgatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcccttttgacatgaacttttctacacactctgagatgtgagggattctttgaatctcgtagtctaatgttcagcttcactggatcttgatatatgcagGATTCTTCTGGTATTTTCTGGGATAACGATAGCTTAGCTGCTCTACTGGCGTTGGAACTGAAAGCTGATCTTCTGATTCTTCTGAGCGATGTTGAAGGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG