Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G70660.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
||| || | | ||| ||| | | | || | | | || | | || || |||| ||| | || || ||| | | | |||||||||||||||||||||| | | |||||||| || |||||||||| || ||||| |||||||||||||| ||||||||||||||||||||||| || |
---------------------------------------------------------------------attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagta-attcatttattga--attctttactgtg-ctgagtacatct---ctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
upper sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
||| || | | | | ||| || | || ||| || ||| | | | | || |||||| | ||| | || ||| | | ||||||||||||||||||||| | | ||||| |||||| | |||||||| || ||||| ||||| || ||||| ||||| ||||||||||||||||| || |
-------------------------------------------------------------ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtgtgataataattta--------gatcata-----ccttgttctatggtgtct--tctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA
upper sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G022859_T01 (Zea mays), 3'ss of exon 1
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
||| || | | | ||| || | || | || || |||| | ||| | | |||||| ||||| | || || | | ||||||||||||||||||||| | | ||||| |||||| | |||||||| || ||||| ||||| || ||||| ||||| ||||| ||||||||||| || ||
-------------------------------------------------------------ttttgttcacaagcacaatgaatttgaactctgaatatctgctattcatgttgc--------ttgataataatttagatcata-----ctttgttctatggcgttt--tctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGACGATGCTGATGACATATT
upper sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
| | |||| || | | | || | ||| || | ||| || | | | |||| |||| | | ||| |||| | | ||| || |||||| || ||||| ||||||||||||||||| || ||||||||||| |||||||||||||| || || || |||||||||||||||||||||||||| |
------------------------------------------------------------taacttatcattgattgtgttcatcttttgttgtaactttttttttttaaatttgtaattggcacc-tatc-ttgtcaaactttt-----tttg------tctatgta---tgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA
upper sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacga-ttttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
|| | | |||| | | | |||| ||||| |||| || | ||| || | | | |||| ||||| | || |||| | || ||| |||||||| || || || ||||||||||||||||| || ||||||||||| |||||||||||||| || || || || ||||||||||||||||||||||| |
-----------------------------------------------------------cttatcactgattgtgttcatct-tttattgtaacttcttttttttttgtaaatttgtaatttgcacc-tatc-ttgttaaa-------atttttggtctat--------gttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA
upper sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G24950.1 (Glycine max), 3'ss of exon 1
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttg--ttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
||||| | | | || | |||| |||| |||| |||| || | | || | | | | |||| || | | || |||| | ||||||||| || || || ||||||||||||||||| || ||||||||||| |||||||| ||||| || || || ||||||||||||||||||||||| || |
---------------------------------------------------------------------attgccttcatcagtc-attgtaagtatttcaattaaacagctttgaaggatttaatagaacttagatttgaaatttactcttcttaattggtccc--------tgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGACATATA
upper sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttg--ttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
| |||| | || || | ||| |||| |||| |||| || | | || | | | | |||| || | | || |||| | ||||||||| || || || ||||||||| ||||||| || ||||||||||| |||||||| ||||| || || || |||||||||||||| ||||| || || |
----------------------------------------------------------------------tgccttcatcagtcatattgcaactatttcaattaaacagctttgaaggatttaatagaacttagatttgaaatttactcttcttaattggtccc--------tgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA
upper sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtg-tggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
|| | | ||| | || | |||| | | ||| | || | | | | | | |||||||| |||||||||| | | ||||||||| || || || |||||| |||||||||| || ||||| || || |||||||| ||||| || || ||||||||||||||||||||||||||||| |
----------------------------------------------------------------------ttatcttggaaaattttc--tggttgttgttgctacatggtcttttgagtgcttgcatg-catagcaggaga--tatatctttg--tgattttgtggtcatatgcagTTCCAAGGAATTTCAGATTACTGGAAGAGCTTGAGAGAGGGGAAAAGGGAATTGGCGATGGAACTGTCAGTTATGGAATGGATGATGCTGATGATATATA
upper sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S311_60V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
| ||| | ||| | ||| || | | ||| | | | || || | | | || | ||||| | | | ||| | ||||||||| || ||||| | | | ||||| || || || |||||||||||||||||||| ||||| || |||||||| ||||| || | ||| ||| | ||
--------------------------------------------------------------------tccaactttccacaatttgag----tagtttcttctaga---actgctgcatttgcgtgttgtgtgattccttagtcctacccttgatagtgtat-tgttatctgcagTTCCAAGGGACTTTCGTCTTCTTGAAGAACTTGAGAGGGGTGAGAAAGGAATTGGAGACGGGACTGTTAGTTATGGCATGGACGACGGTGACGATGTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
gattgat putative branch site (score: 4)
attgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT