Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgttcaagctacaattcaatcatcatagtgaaattgcaacactaaagttgaaaattagagaaatttgagactgctttactgacggttgatttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G40810.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 4
gtgagtgttcaagctacaattcaatcatcatagtgaaattgcaacactaaagttgaaaattagagaaatttgagactgctttactgacggttgat--ttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG
||| || || || | | | | | | ||| | ||| ||| || || | |||| | |||| ||| || || ||||| || ||||||||| ||||| ||||| ||||||||||| ||||| | || || |||||||| ||||| ||||| |||||||| ||
-------atcacaatattcttttgctcccaagaaaatccttttaaccactactaccctattcttgctgttt---actcattgtcttatatttgaacacttctatgatcagTATTCGGCGTGGACATCAAGTTTATACACAAGTGTGTGCCTCTTGCCATTCCATGTCATTAATTTCGTACCGAGATTTGGTTGGTGTGGCCTACACTGAA
upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G22530.2 (Glycine max), 3'ss of exon 3
gtgagtgttcaagctacaattcaatcatcatagtgaaattgcaacactaaagttgaa-aattagagaaatttgagactgctttactgacggttgatttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG
|| || | ||| | | || || ||| || | | | || || | | | | |||| | |||||| |||||||||||| ||||||||||| ||||||||||| |||| ||||| ||||| ||||| |||||| |||| |||||||| || ||||| |||||||| || |||||
-----ccaccatcatatggtcaaattaattttgt----tttttacatgaatgctatataactatttatactaattgaggtcttacagttaactgattttgaatgagcagGATTCGTCGTGGTCATCAAGTTTATCAAGAAGTCTGTGCTTCTTGTCATTCTATGTCTTTGATATCATACCGTGATTTGGTTGGTGTTGCTTATACAGAA
upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 3
gtgagtgttcaagctacaattcaatcatcatagtgaaattgcaacactaaagttgaaaattagagaaatttgagactgctttactgacggttgatttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG
||| | ||| | ||| | | | | || || ||| | | | ||| | ||||| | |||| | |||| ||| |||||||| ||||||||||| ||||||||||| |||| ||||| ||||| ||||| |||||| |||| |||||||| || ||||| |||||||| || |||||
--ccaccctcatatttcaaattaattgtttttttttacatg-aatgctata--taactatttatactaattgag---gtcttacagttaaccaattttgaataagcagGATTCGTCGTGGTCATCAAGTTTATCAAGAAGTCTGTGCTTCTTGTCATTCTATGTCTTTGATATCATACCGTGATTTGGTTGGTGTTGCTTATACAGAA
upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G06700.1 (Glycine max), 3'ss of exon 4
gtgagtgttcaagctacaattcaatcatcatagtgaaattgcaacactaaagttgaaaattagagaaatttgagactgctttactgacggttgatttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG
| | || | | | | ||||| || | ||| | | | | | || ||| | ||| | | | || | || |||| | ||| ||||||| ||||||||||| ||||||||| |||| ||||| || |||||||| |||||| |||| || || || || ||||| |||||||| || |||||
----gaatacatgttctgctgctatcat-gtatttaaacc---atatttcacgttaagtttatattaatatcaattcttaatgctttcaattaatttttcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA
upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 3
gtgagtgttcaagctacaattcaatcatcatagtgaaattgcaacactaaagttgaaaattagagaaatttgagactgctt-tactgacggttgatttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG
|| || | | | |||| ||| | || | ||| | || || | ||| | | | | | | | | || | || |||| | ||| ||||||| ||||||||||| ||||||||| |||| ||||| || |||||||| |||||| |||| || || || || ||||| |||||||| || |||||
-------tttaaaccatatttca--cattaaggttatattagtatctataatttaataataattaacgccttaaattcttaatgctttcaattaatttttcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA
upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtgttcaagctacaattcaatcatcatagtgaaattgcaacactaaagttgaaaattagagaaatttgagactgctttactgacggttgatttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG
| | | | || || | || | ||| | | | ||| || ||| | ||| | || | | | | | |||||| | || |||||| || || |||||||| ||||| |||||||||||||| ||||||||||| |||||| | || |||| || || | |||||||| || ||||| ||
--gttcctctatggaggaacacatttat----gcaaaaattccatcttaatttttcccattctctcagttttac-ttgatacatttatg-ctgattttacaagaacagGATTCGGCGGGGTCACCAGGTTTACCAGCAAGTTTGTGCTTCTTGCCATTCAATGTCTTTAATTTCATTTCGTGATCTTGTGGGTGTGGCATACACTGAA
upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 3
-gtgagtgttcaagctacaattcaatcatcatagtgaaattgcaacactaaagttgaaaattagagaaatttgagactgctttactgacggttgatttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG
||| || || ||| | | ||| ||| || ||| |||| | | || ||| ||| || | || ||||| |||||||| |||||||||||||| ||||| || ||||| ||||| || |||||||| ||||| || || ||||| || || || |||||||| || || |||||
tttgatctatctagggccaaactttttgttatatc----ttgggtcattaatcttgatatcaatttctcaatgcaactttttttatgccaatttatttg-----agcagGATTCGTCGTGGTCACCAGGTTTACCAACAAGTCTGTGCATCCTGCCATTCTATGTCACTAATTTCATATCGTGATTTAGTGGGTGTGGCATATACAGAAMapped 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|124980747|gb|EL053676.1|EL053676EST: CCCTTGGCCACATGAGGGCATTCTCAGCTCATATGACCATGCTTC GATCCGTCGTGGTCACCAAGTTTATCAGCA
genomic: CCCTTGGCCACATGAGGGCATTCTCAGCTCATATGACCATGCTTCgtgagtgttc ... taatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaattagagaaatttgagactgctttactgacggttgatttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG
atttgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgttcaagctacaattcaatcatcatagtgaaattgcaacactaaagttgaaaattagagaaatttgagactgctttactgacggttgatttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG