Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtcccttacctaactccttcaatgatcacatagcgataatgttgctaatttcgaagcccttacacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G33340.2 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G33340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 15
-------------gtaaagtcccttacctaactccttcaatgatcacatagcgataatgttgctaatttcgaagccct----tacacttg---cagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA
|| | || || | | | | || | || | | ||||||| | | | ||||||| |||| |||| || || |||||||| | ||||| ||||| |||| || ||||| ||||| |||||||||||||||||||| | ||| || || || |
gttcgtccctttcttatggcccacattctcggttcgtgattggcatctgtgcttgcacttaactaatttggtttctgtggcgtacacttttctcagGGAAAGTGACAAACGTCAAGTTTGGCACCGATGCGAAGTACATTGCCGTAGGTTCTATGGATCGTAACCTACGGATATTTGGGCATCCGGGAGAAGATGA
upper sequence: AT2G33340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G324540_T01 (Zea mays), 3'ss of exon 17
-----------------gtaaagtccctta-cctaactccttcaatgatcacatagcgataatgttgctaatttcgaagcccttacactt--gcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA
| |||| ||| || | |||| | || |||| || | | | | | || ||| |||| |||| || | || || || || ||| || | ||| | || | ||||| |||||||| || ||||||||||||||||| ||||| ||||| |
gtgtgtccctctttttaccatagtctcttggtgcaatttcttcttagttcttggagcgcacattgacttggtgttgtgacatttgtccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAGGTTCTATGGACCGCAATCTACGGATATTTGGTCTCCCTGGAGATGATCA
upper sequence: AT2G33340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G324540_T02 (Zea mays), 3'ss of exon 16
----------------------------------------gtaaagtccctta-cctaactccttcaatgatcacatagcgataatgttgctaatttcgaagcccttacactt--gcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA-----------------------
| |||| ||| || | |||| | || |||| || | | | | | || ||| |||| |||| || | || || || || ||| || | ||| | || | ||||| |||||||| || ||||||||||||||||| ||||| ||||| |
attacccgatttatcaggaacaggtgtgtccctctttttaccatagtctcttggtgcaatttcttcttagttcttggagcgcacattgacttggtgttgtgacatttgtccttccacagggaaagtaacttccgtaaaattcGGAGTAGACGCGAAATACATAGCCATAGGTTCTATGGACCGCAATCTACGGATATTTGGTCTCCCTGGAGATGATCAAATGGAGGAATCAAACACAGCGGMapped 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|124953130|gb|EL028347.1|EL028347EST: CTCCGGCACTG GTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCG
genomic: CTCCGGCACTGgtaaagtccc ... acacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCG
EST:
gi|124955811|gb|EL030793.1|EL030793EST: GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGNTCTCTCCGGCACTG GTAAAGCTACGTG
genomic: GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGATCTCTCCGGCACTGgtaaagtccc ... acacttgcagGTAAAGCTACGTG
EST:
gi|124731446|gb|EH822848.1|EH822848EST: GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGATCTCTCCGGCACTG GTAAAGCTACGTGTGTGAAGTTTGGTT
genomic: GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGATCTCTCCGGCACTGgtaaagtccc ... acacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcaatgatcacatagcgataatgttgctaatttcgaagcccttacacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA
cccttac CT-rich tract
ataatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtcccttacctaactccttcaatgatcacatagcgataatgttgctaatttcgaagcccttacacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA