Sequence
atgc intronic sequence ATGC exonic sequencegttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G57290.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g07250.1 (Oryza sativa), 3'ss of exon 1
gttgtgatttggatgattaagttgtttaattttgt-gaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
| |||| | | || ||||| | |||||| | | ||| | | | || ||| | | || | |||| ||| |||| | | | ||||||||||| || ||||||||| || |||| ||||| ||||| ||||||||||| ||||| || || || ||||||| | || | | || ||| |
-tcttgatattccccttcaa-ttgttaatttttgtagttaccatatgccaagtcatttaggttgctatgcagttaat----aatcgtatt---cttgttaacattgcagATTGGTCCTGATCAGATTGAGACTCTGTATCAGTATGCCAAATTTCAGTTTGACTGTGGGAATTACTCATTTGCTGCTCAGTACTTGCATCAATACCGTG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g32040.1 (Oryza sativa), 3'ss of exon 1
-gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggct--tggtgtcttat-cagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
|| || | | || || || | | | | | | |||| | | | || || | | | | | | | | ||| ||| ||||||||||| || ||||| |||||| |||| ||||| |||||||||||||| || || || ||||| | | ||||||||| | | | | ||| |
gttttctcttccgctagctagatttgttcttcgtctatataatcgccatgattatatatccatagta-ataatcgtatgcgttcttggggtaattaacgatgtgatatgcagATTGGTCCTGATCAGATCGAGGCTCTGTATCAGTATGCCAAGTTTCAGTTCGACTGCGGGAACTACCCAGATGCTGCTGAAAACTTGCATCGATACCGTG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g12110.1 (Oryza sativa), 3'ss of exon 1
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
|| || |||||| ||||| | | | ||| | | | | | | | |||| ||| ||| |||| | | | || | ||||||||||| || ||||||||| || |||| |||| ||||||||||||||||| || || || || || | |||||||| || | || || ||| |
---gttgttaccatgatt---ttgttaagtcggttagcatgctgtatacttattgcat-gtttttgtgcgacccaac-taaataatcaaactcctgttaatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTTGACTGCGGTAATTACTCAGATGCTGCTGTCTACTTGTATCAATACCGTG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G107893_T01 (Zea mays), 3'ss of exon 4
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttat-cagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
| ||| |||| ||| || | ||| | | |||| | | | | || |||||| || | | | ||| | |||| | | || ||||| ||||| ||||||||||| ||| |||| ||||| ||||| ||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |
-tcaaaattcagatgg----aacgttgaagct-gtgcatttttatt--gctatagcttgttttgtg-ataattgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 1
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttat-cagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
||| ||||| | |||| | | || || || | | | | | || |||||| || | | ||| | |||| | | || ||||| ||||| ||||||||||| ||| |||| ||||| ||||| ||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |
--caaaattcagatgaa-acgttga--agctgtgc---attttttattgctatagcttgttttgtgataaatgcta-atgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G132144_T01 (Zea mays), 3'ss of exon 5
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttat-cagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
| ||| ||||| ||| || | | | | | |||| | | | | || |||||| || | | ||| | |||| | | || ||||| ||||| ||||||||||| ||| |||| ||||| ||||| ||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |
-tcaaaattcagatga----aacgttgaagct-gcgcatttttatt--gctatagcttgttttgtgataaatgcta-atgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G038028_T01 (Zea mays), 3'ss of exon 6
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttat-cagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
| ||| ||||| ||| || | ||| | | |||| | | | | || |||||| || | | ||| | |||| | | || ||||| ||||| ||||||||||| ||| |||| ||||| ||||| ||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |
-tcaaaattcagatga----aacgttgaagct-gtgcatttttatt--gctatagcttgttttgtgataaatgcta-atgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G094083_T01 (Zea mays), 3'ss of exon 8
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttat-cagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
| ||| ||||| ||| || | ||| | | |||| | | | | || |||||| || | | ||| | |||| | | || ||||| |||| ||||||||||| ||| |||| ||||| ||| | ||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |
-tcaaaattcagatga----aacgttgaagct-gtgcatttttatt--gctatagcttgttttgtgataaatgcta-atgaattgatcaatccttgtttaccaatgcagATCGGTCTTGACCAGATTGAAGCTCTGTATCAGTATGCCCAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G038313_T01 (Zea mays), 3'ss of exon 1
--gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
| ||| |||| |||| || | ||| | | |||| | | | | | | |||| || | || || || || | | | ||||||||||| ||||||||||| ||| |||| ||||| ||||| ||||||||||| ||||| ||||| || | |||||||| || || |||||||| |
agatcaaaattcagatgg----aatgttgaagct-gtgcacttttatt--gttatagcctcttctgtgctaaatgcta-acgaac--taaatccttgtttaacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCCTGGGCTGCTGAGTACCTGTACCAGTATCGTG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G105461_T01 (Zea mays), 3'ss of exon 2
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA---------------
| | | || | || | | ||||| | | | | | | | ||| | || | | | |||| || | | |||| ||| |||| ||||| ||||| ||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |
-------------ggcacagatagtctcatctcatag--------tcagatccagcctc-tccgaatctggccaggtgtgt-tctggtttgctctatttttttatatacttatataatatagcCTTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTGCTTTGTGCACAAACA
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G156333_T01 (Zea mays), 3'ss of exon 4
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttat-cagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
| ||| ||||| ||| || | ||| | | |||| | | | | || |||||| || | | ||| | |||| | | || ||||| | ||| ||||||||||| | | |||| ||||| ||||| ||||||||||| ||||| ||||| || || |||| |||||| ||||||||||| |
-tcaaaattcagatga----aacgttgaagct-gtgcatttttatt--gctatagcttgttttgtgataaatgcta-atgaattgatcaatccttgtttaccaatgcagATAGTTCCTGACCAGATTGAAGTTGTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGTTGATTACCTTTACCAGTATCGTG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 2
--gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
||| | | | | | || || | ||| ||| | | | |||| | || || || ||| || | | ||| | || | ||||||||||| | ||||| || || |||||||| || ||||| || |||||||| ||||| ||||| |||||||||||||| |||||||| ||||||||
ctgttttagtggttttaaaagaattattctacttttggaagt----ttgaattttg---tggtatgagtcctgtctgac-tatgtaaacaatgattc--tgctgaaacagATTGGTCCTGCACAGATAGAAGCGTTGTACCAATATGCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAGTACAGAG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
-gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
| ||| ||| || | || | | | || | | | || || || |||||| ||||| | ||| || || || || || ||||||||||| | ||||| || || |||||||| || |||| || |||||||| ||||| ||||| |||||||||||||| |||||||| || |||||
tgctgtattttagaggttttaaaagaatcatcct----agttttgagaag-ttgaattttgtg---gtatttgagttcactgtgtaaatgaggattc-tgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
upper sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 3'ss of exon 2
gttgtgatttggatgattaagttgtt--taattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
| || ||| | || || ||||| |||||| ||| || ||||| | | |||| || || | ||| | | || | ||| | |||||||| | || ||||| ||||| || || ||||| ||||| ||||||||||||||||| ||||| ||||||||||||||||| || || |||||||||
-tcctgtttttgttg-ttgtattgttgctaatttgacagaattctaggtt--tttgggtctatttggc--ttacaaaat-tatatcccttttttct---tttctgaccagATTGGCCAGGAGCAGATAGAGGCATTATATCAGTATGCCAAATTTCAGTTTGAATGTGGAAACTACTCTGGTGCTGCTGATTACCTGTATCAGTACAGGGMapped 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|86078869|gb|DR374626.1|DR374626EST: TAAGAGCTGACAAGCAGTACAATCTCCAAATGCTCAAGGAACGCTACCAG ATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTT
genomic: TAAGAGCTGACAAGCAGTACAATCTCCAAATGCTCAAGGAACGCTACCAGgttgtgattt ... gtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
tcttatc CT-rich tract
aaatcttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT