Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgaaaaaaagtgatttcaactactgtcttagtttctgcttattgaggatttcttcttaactaaaggttgtggctttttcacctatagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGTCCTGGACTGAGATTTACTGTTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10270.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 4
gtttgtgaaaaaaagtgatttcaactactgtcttagtttctgcttattgaggatttcttcttaactaaaggttgtggctttttcacctatagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGTCCTGGACTGAGATTTACTGTTCC
|| || | | | | ||| | || || || | | ||| | | | | | | | | || | | || |||||| |||||||| ||||||||||||| || |||||||||||||||||| | ||||| || |||||| | ||||| || | || |||||
gtatggcacattttattcctgcaattccttggtttgtgggagtggttctaggttgtaatgtctgatgcattgtcatcttgttgaaatagTCGAGGGTAACAAGTACAAGGGGAGCATCTACATGGTCTTCGAGTACATGGATCATGATCTTACTGGGCTTGCAGATAGGCCTGGGATGCGGTTCACTGT---
upper sequence: AT5G10270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g32360.1 (Oryza sativa), 3'ss of exon 4
----gtttgtgaaaaaaagtgatttcaactactgtctt--agtttctgcttattgaggatttcttcttaactaaaggttgtggctttttcaccta-tagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGTCCTGGACTGAGATTTACTGTTCC
| | | |||| | ||| | | | | | ||| |||| ||| |||| || ||| | | ||||| | | || | || |||||| |||||||| |||| |||||||| || ||||||||||| ||||| |||||||| | |||||| | ||||| || | || || ||
gtacggctttttaaaagaacgataaatattgatattcttgggttgctgcatat-----atttttttttatgttgaagttgttatgtcgttgtatagTCCATGGTAACAAGTACAAGGGGAGCATTTACATGGTCTTCGAGTACATGGACCATGACTTGACTGGGTTGGCAGATAGGCCTGGGATGCGTTTCACCGT---
upper sequence: AT5G10270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G028452_T01 (Zea mays), 3'ss of exon 3
--------------gtttgtgaaaaaaagtgatttcaactactgtcttagtttctgctt--attgaggatt-----tcttcttaactaaaggttgtggctttttcacctatagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGTCCTGGACTGAGATTTACTGTTCC
| | | ||| ||| ||| || | || || | | || ||| | | | || | || || | ||||| | | || | ||||| |||||||| |||| ||||||||||| ||||| ||||||||||| | ||||| || || ||| | || ||| || | || | |||
gtcaagtatggcgagctctatcttgtgattgagttccactgctttattttttagggttaagatagagcaatggtaatgtttggcatgaattatttgtgttttttaattagTTGACGACAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGATCATGACCTCACTGGGCTTGCTGATAGACCAGGAATGCGGTTCATTGT---
upper sequence: AT5G10270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G028452_T02 (Zea mays), 3'ss of exon 3
---------gtttgtgaaaaaaagtgatttcaactactgtcttagtttctgctta--ttgaggatt-----tcttcttaactaaaggttgtggctttttcacctatagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGTCCTGGACTGAGATTTACTGTTCC
| | | ||| ||| ||| || | || || | | | | ||| | | | || | || || | ||||| | | || | ||||| |||||||| |||| ||||||||||| ||||| ||||||||||| | ||||| || || ||| | || ||| || | || | |||
gtatggcgagctctatcttgtgattgagttccactgctttattttttagggttaagatagagcaatggtaatgtttggcatgaattatttgtgttttttaattagTTGACGACAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGATCATGACCTCACTGGGCTTGCTGATAGACCAGGAATGCGGTTCATTGT---
upper sequence: AT5G10270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0141g00280.t01 (Vitis vinifera), 3'ss of exon 4
-------------------gtttgtgaaaaaaagtgatttcaactactgtcttagtttctg--cttattgaggatttcttct-------taactaaaggttgtggctttttcaccta-------tagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGTCCTGGACTGAGATTTACTGTTCC
| | | | | | |||| | | | || ||||||| ||| | | ||| | | || ||| | | ||||| | | ||||| ||| ||||||| ||||||||||||||||||||||| |||||||| |||||||| | || || | ||||||||||||||||||||| | ||||
gtgagtggagctgttgcatggtgtccacttagaattatttaagttcttttcatagtttcctattttacttaaagtttatgccatgggagtatttaacatgaatcgttttttttcttggagactttagATGGTAATAAATACAGAGGTGGCATCTACATGGTTTTTGATTACATGGACCATGATTTAGCAGGCCTGTCTGATCGTCCTGGACTGAGATTTTCAATTCC
upper sequence: AT5G10270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0805g00020.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gtttgtgaaaaaaagtgatttcaactactgtcttagtttctg--cttattgaggatttcttct-------taactaaaggttgtggctttttcaccta-------tagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGTCCTGGACTGAGATTTACTGTTCC
| | | | | | |||| | | | | ||||||| ||| | | ||| | | || ||| | | ||||| | | ||||| ||| ||||||| ||||||||||||||||||||||| |||||||| |||||||| | || || | ||||||||||||||||||||| | ||||
gtgagtggagctgttgcatggtgtccacttagaattatttaagttctttttatagtttcctattttacttaaagtttatgccgtgggagtatttaacatgaatcgttttttttcttggagactttagATGGTAATAAATACAGAGGTGGCATCTACATGGTTTTTGATTACATGGACCATGATTTAGCAGGCCTGTCTGATCGTCCTGGACTGAGATTTTCAATTCC
upper sequence: AT5G10270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------------------------------------gtttgtgaaaaaaagtgatttcaactactgtcttagtttctgcttattgaggatttcttcttaactaaaggttgtggctttttcacctatagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGT---CCTGGACTGAGATTT-ACTGTTCC
|| | ||| ||| | | | | | | | ||| || |||||| | ||||| | || ||||||| | || | | | | | | | ||| |||| | | | | | | | | | | | || | | | | ||| | ||||| ||||| |||| |
gtgggcgctgattttatcatcgtcttatgtatgcgtacatgaactatatgtcgatagacgtctctctgtattctgagcatgtcattattgctgaggatttggttctttctttcaaatgagtagtc-cgatgaatatatattttttgattttgtgaggacacat-----actaagcgcagttgcttttt-atttaaacagGACCAGAGA-AGGAGGACAACATCAAGCCAGGTGAAGCGAATAAGTTCAAAGGGTCGATTTACATGGT-GTTCGAGTACATGGACCATGATTTGACTGGCCT
upper sequence: AT5G10270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S235_102V6.1 (Physcomitrella patens), 3'ss of exon 3
---gtttgtgaaaaaaagtgatttcaactactgtcttagtttctgcttat----tgaggatttcttcttaactaaaggttgtggctttttcacctatagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGT--CCTGGACTGAGATTT-ACTGTTCC
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ataatcaccactactgggtaatgtcaactggaaattcgtgcttcgataacagcgtgtgaaattctcccttggtgaaaga-gttgtctttggatgtgaaca-gGTCCTGAGAAAGAGGACAACATCAAGCCAGGTGATGCGAGTAAGTTCAAAGGCTCTATTTACATGGTGTTTGAGTACATGGACCATGATTTGACTGGCCTMapped 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|124910485|gb|EH984565.1|EH984565EST: GTCGGGACAGGGATGACCAAGGAAAGCCAG ATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTA
genomic: GTCGGGACAGGGATGACCAAGGAAAGCCAGgtttgtgaaa ... tcacctatagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgcttattgaggatttcttcttaactaaaggttgtggctttttcacctatagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGTCCTGGACTGAGATTTACTGTTCC
aactaaa putative branch site (score: 2)
ctttttcacct putative PPT
ttaactaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgaaaaaaagtgatttcaactactgtcttagtttctgcttattgaggatttcttcttaactaaaggttgtggctttttcacctatagATAATAACAAATACAAGGGTGGCATCTACATGGTTTTTGAGTACATGGATCATGATTTGACTGGACTAGCAGATCGTCCTGGACTGAGATTTACTGTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT