Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtccccaattcaatttgaactttgtgttacctaaactagttttagtgaattggttttgtgctagcagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G20110.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G20110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g50840.1 (Oryza sativa), 3'ss of exon 1
------------------------gtaatgtccccaattcaattt---gaactttgtgttacctaaactagttttagtgaattggttttgtgct-agcagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA
| ||| | || | | ||| || | | | ||| | | ||||| | | ||||| ||||||||||||| |||| ||||||||||| | |||||| | || ||||||||||| || ||||| | | || ||||| ||
gtgaagttttacgctgttgtacttattgtgtacttgcgtctactcctggaatgacccaataatcattattttattacttatctggttgtaccttgagcagGTTGGTTTGGATGGGATTCGGATGCTTGATCCCAATACTAGTAGGACATTGAGAATATACCCCCTTGAAACTGTAACTAGATGGGAT
upper sequence: AT1G20110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G02550.1 (Glycine max), 3'ss of exon 1
------------------------gtaatgtccccaattcaatttga--actttgtgttacctaaactagttttag-tgaattggt-tttgtgctagcagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA
| || | || | ||| || || ||||| | | | | | ||| | ||| ||||||||||||||||| |||||||||| ||||||| ||| ||||| || |||||||| ||||||||||||||||| |||||||| ||
tctttctatatattcctgattttgtttttgcttctaaaaaatgttggtcacattatgttattgctgttgatctgaacttcgttgacctctgtctgctcagATTGGTTTGGATGGAATTCGTATGCTGGATCCAAATACCAGCCGGACATTGAGAATTTATCCTCTTGAGAACATAACAAGATGTGAT
upper sequence: AT1G20110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G37890.1 (Glycine max), 3'ss of exon 1
----------------gtaatgtccccaattcaatttgaactttgtgttacc-------taaactagttttagtgaattggt-----tttgtgctagcagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA
| || || | ||| ||| |||| | | | ||||||| || || | | || ||||| ||||||||||| |||||||| | ||||||| |||||| ||||| |||||||||||||| ||||||||||| |||||||| ||
tagcataattttttatatgcattcattaaactattttctgtttttcactaccatggtggttgatctgaattagtgattttgtcaatgctaattctttcagATCGGTTTGGATGGAATTCGTATGTTGGATCCAAATACTAGTCGAACATTGAGAATATATCCACTTGAGAACATAACAAGATGTGAT
upper sequence: AT1G20110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G02510.2 (Glycine max), 3'ss of exon 1
------------------------gtaatgtccccaattcaatttga--actttgtgttacctaaactagttttag-tgaattggt-tttgtgctagcagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA
| || | || | ||| || || | ||| || | | | | || ||||| ||||||||||||||||| |||| ||||| ||||||| ||| ||||| || |||||||| ||||||||||||||||| |||||||| ||
tttcatagaaaattcctgatcttatttttgcttctaaaatatgttggtcacattatcttattgctgctgatctgaactctgttaacctttgtctgctcagATTGGTTTGGATGGAATTCGCATGCTGGATCCAAATACCAGCCGGACATTGAGAATTTATCCTCTTGAGAACATAACAAGATGTGAT
upper sequence: AT1G20110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G40250.1 (Glycine max), 3'ss of exon 1
----------gtaatgtccccaattcaat--ttgaactttgtgttaccta-------aactagttttagtgaattggttttgt----gctag------cagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA
|||| | || || | || |||| | |||| || | ||||| | | | |||||| |||| ||||||||||||||||| |||||||| | ||||||| |||||| ||||| |||||||||||||| |||||||||| |||||||| ||
gacatttagcataatttttgttatgcattcattaaactatttgttgtttaccatggtggttgattttaattggt-gattttgtcactgctaattctttcagATTGGTTTGGATGGAATTCGTATGTTGGATCCAAATACTAGTCGAACATTGAGAATATATCCAATTGAGAACATAACAAGATGTGAT
upper sequence: AT1G20110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g14750.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------gtaatgtccccaattcaatttgaactttgtgttacctaaactagttttagtgaattggttttgtgctagcagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA
| | || || || | | | || | | | ||| || ||| || || | | ||||||||||||||||| ||||||||||||| || || ||||| ||||| |||||||||||||| ||||||| || |||||||| |||
atataatataagtgccaagttttgttttgcttctttctcctttttattgcatatttactaatttttttactcaccttt-tgatttatgattttcatctcagATTGGTTTGGATGGAATTCGTATGCTTGAACCCAGCACTAGTCGAACATTGAGAATATATCCACTTGAGACAATAACAAGATGTGAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125248396|gb|EL262481.1|EL262481EST: AACAGATGTTCTTTGTCAG ATTGGTTTGGTTGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTG
genomic: AACAGATGTTCTTTGTCAGgtaatgtccc ... gtgctagcagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTG
EST:
gi|86068172|gb|DR363929.1|DR363929EST: AATTGTTGGCTGAGACTTATGGACAAACCACAACAGATGTTCTTTGTCAG ATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTG
genomic: AATTGTTGGCTGAGACTTATGGACAAACCACAACAGATGTTCTTTGTCAGgtaatgtccc ... gtgctagcagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgaactttgtgttacctaaactagttttagtgaattggttttgtgctagcagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA
acctaaa putative branch site (score: 3)
tagtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtccccaattcaatttgaactttgtgttacctaaactagttttagtgaattggttttgtgctagcagATTGGTTTGGATGGTCTTCGTATGCTTGATCCAAGTACTAGCCGAACTTTGAGAATATATCCTCTTGAGAACATCACAAGATGCGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG