Sequence
atgc intronic sequence ATGC exonic sequencegtatacgttgttaatacattgaacatcagtagccactgacttttctttgtgctaactgactctcgttttgtgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46630.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------------------gtatacgttgt-taatacattgaacatcagtagc-cactgacttttctttgtgctaactgactctcgttttgt----gcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
||||| || | | || | | ||| || | | ||| | | |||| | |||| |||| ||| || || |||||||||||||||||||||||||| ||||||||||| ||| |||| ||||| ||||| || ||||| || || ||||| || || || ||
gtatcactttatcaataattagtacatgaagaaaaaaaattgagcatctggtttttctgattagtatagtttatatggtatgtacacaatctttactactttaactgaattgtctgctggtcggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 7
------------gtatacgttgttaataca-----ttgaacatcagtagccactgacttttct----ttgt-gctaactgactctcgttttg---tgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
|| | | |||||||| || | | |||| || |||| || | || ||| | ||| | |||||| || || || || ||||||||||||||||| ||||||||||| ||| | || ||||| ||||| || ||||| || ||||| || ||||| || ||
cagatcgtggtagttttgctcattaatacaatttttttggaacttttttttgtcatctttgctaaatttgttactgattgtgtcttctcttgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G16630.2 (Glycine max), 3'ss of exon 6
--------------------------gtatacgttgttaatacattgaacatcagtagccactgacttttctttgtgctaactgactctcgttttgtgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
| || || | | | | | | | ||||| | | || | || || | ||||||||||||| || ||||||||||||||||| || || || ||||| || |||| || |||||||| |||||||||||||||||||||||||| |||||
attctgtatggtgtacttggagggcattttatcctgctgtttggtctctttccctattctaatcactttcccccct-cttatcaacaaatgtatgttgcagTGGTAAAAGTATCGAGCTTGATGATGTCACTTTCCATCAATGTGTAAATTTGACAAGGTTCAACTCAGAGAAGACTGTTAGTTTTGTACCACCTGATGGT
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 7
-------------------------gtatacgttgttaatacattgaacatcagtagccactgacttttctttgtgctaactgactctcgttttgtgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
| | || | | | | | | | | | | || | | ||||||||||||| || ||||||||||||||||| || || || ||||| || |||| || |||||||| |||||||| ||||||||||||||||| |||||
gctgtacttggaggttattttatcctcctgtttggtctctgtccctgttctaattgctcccccccccccccccccccccatcaacaaatctatgatgcagTGGTAAAAGTATCGAGCTTGATGATGTCACTTTCCATCAATGTGTAAATTTGACAAGGTTCAACTCAGAGAAGACAGTTAGTTTTGTACCACCTGATGGT
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 7
------------------gtatacgttgttaatacattg-----aacatcagtagccactgacttttctttgtgctaactgac--tctcgttttgtgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
||| || ||| ||| | | ||| || | | |||| | || | |||||| ||||||||||||||||||||||| || || |||||||| || || |||| || || ||||| || ||||| || |||||||| ||||| |||||
tacagttttgtttatcacatatttatttcaaatggcttgttttaggctgtgatgttggttgatttgataacttagtctctgataatgctaccttttacagTGGCAAAACCATTGAGCTTGATGATGTTACTTTCCACCAGTGCGTAAATTTGACGAGGTTTAACTCAGAAAAGACCGTCAGTTTTGTGCCACCAGATGGT
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------------------------------gtatacgttgttaatacattga-acatcagtagccactgacttttct---ttgtgctaac-tgactctcgttttgtg-cagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
| | || | | || | || | | | || | |||||| |||||| ||| || |||||| ||||| ||||||||||||||||| ||||| ||||| ||||| || || || ||||||| | |||||||| || |||||||| ||||| ||||||
gttgaatgcgcatccacactcttgtgatggcttcgtttaacaatgttgccctcaagtgttttttatttttatttttattttatttactttattttttactctcattctcttgcagcttcgacatatttgggtttgaaaagtgttttacactgtgctcttgtgactcctctttcatgacagTGGGAAAACAATTGAGCTTGATGATGTTACATTCCACCAATGTGTCAATCTCACAAGATTCACTGCTGAGAAGACAGTCAGTTTTGTTCCACCCGATGGA
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------------gtatacgttgttaatacattgaacatcagtagccactgacttttctttgtgctaactgactctcgttttgtgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
| | || ||| ||||| || | || ||| ||| || || | | | | ||| |||||| || || |||||||||||||| |||||||| |||||||||||||| || || |||||||| |||||||||| || ||||| || ||||||||||||
gttgaatgcacattcctggggcaccctgattttgctatggcttcattgtgcaaagtttccccgagatgcttctttccccttgcagatttgaaatgt-ttgaaaattggaaggtacttgacattcc--gtcctgatgtatttccttttacgacagTGGCAAGACAATTGAGCTTGATGACGTCACATTCCACCAGTGTGTGAATCTTACGAGATTCAATGCCGAGAAGACAGTCAGTTTCGTTCCACCGGATGGA
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 7
gtatacgttgttaatacattgaacatcagtagccactgacttttctttgtgctaactgactctcgttttgtgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
|| | | |||| || |||| ||| || ||| | || ||| || | |||||| ||||| || ||||| || |||||||| ||||| ||||| || ||| | |||||||| |||||||||||||| || || ||||| || |||||||||
--gtatgct-ttaagg---tgtacattagtg-----caacctttttgattgataa---------aaatttttcagTGGGAAAACGATAGAGCTGGACGATGTCACGTTTCATCAGTGCGTCAACTTAACCAGATTTAACTCCGAGAAGACGGTCAGCTTTGTTCCTCCGGATGGA
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 7
gtatacgttgttaatacattgaacatcagtagccactgacttttctttgtgctaactgactctcgttttgtgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
|| | | |||| || |||| ||| || ||| | || ||| || |||||||| ||||| || ||||| || |||||||| ||||| ||||| || ||| | |||||||| |||||||||||||| || || ||||| || |||||||||
--gtatgct-ttaagg---tgtacattagtg-----caacctttttgattgataa---------aaattttgcagTGGGAAAACGATAGAGCTGGACGATGTCACGTTTCATCAGTGCGTCAACTTAACCAGATTTAACTCCGAGAAGACGGTCAGCTTTGTTCCCCCGGATGGAMapped 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|124890954|gb|EH969856.1|EH969856EST: AAAATTGGTCTTGAGAAGGAATCAGAAATGAAATCTCGCCCAGCTAAGAG TGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGA
genomic: AAAATTGGTCTTGAGAAGGAATCAGAAATGAAATCTCGCCCAGCTAAGAGgtatacgttg ... ttttgtgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacatcagtagccactgacttttctttgtgctaactgactctcgttttgtgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
ctctcgtttt CT-rich tract
ttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacgttgttaatacattgaacatcagtagccactgacttttctttgtgctaactgactctcgttttgtgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA