Sequence
atgc intronic sequence ATGC exonic sequencegtatatctctctataagggcgaaatcttgatttcatgattgtatcttcagcggtttctgtgttccttaaaatgagtttttgttttgaacagGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAAGAAGCTTTCATGGCCGTTCTCAAACTTGAACGAGAAGTATTGTGACATC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08650.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 21
-------------------------------------gtatatctctctataagggcgaa-atcttgatttcatgattgtat---cttcagcggtttctgtgttccttaaaatgagtttttg----ttttgaacagGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAAGAAGCTTTCATGGCCGTTCTCAAACTTGAACGAGAAGTATTGTGACATC
| | | | ||| | ||| | | | | | | | ||| || || || | | | |||| |||| || ||||||| | || ||||||||||||||||| ||||| || |||||||| |||||||| || || ||||| || | ||||| ||| || || | ||| |
gtaagccttctccacaaccatctcagattcaaataagttttttttttcttttggggtgcttagccaaagctagtagctttattcactatcgccaattagagataagatgatatgaccatttgacatttcccaacagGCTGAGGGAAAGAAGAGAATGAAAGCAATAGGAAGGGTTGATGTTCCTCAAGAGGCATTTATGGCTGTGTTGAAACTAGAAAAGGAGGTGCTATGAAACA
upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G003157_T02 (Zea mays), 3'ss of exon 12
---------------------------------------------------------------------------------------gtatatctctctataagggcgaaatcttgatttcatgattgtatcttcagcggtttctgtgttccttaaaatgagtttttgttttgaacagGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAAGAAGCTTTCATGGCCGTTCTCAAACTTGAACGAGAAGTATTGTGACATC
| || | | ||| || ||| | | | | | | | || || | | || | | | |||||||| | ||| ||||| || ||||| || ||||| || |||||||||||||||||||| ||||||||||| | | ||| ||| || || | ||| |
gtattcttagaaaaaaacgttgtttgaccccaaaaaaaagaacttagaaaataccattttgtgtataatacataagcagtatactggctttaagttttcatagaatacaagaaatgacta-gtagctctgttcaccaaaatccctttgagatctgatataa--taatacggcgaacagGCTGAAGGAAAGAAAAGGATGAAGGCAATAGGAAGGGTTGATGTCCCTCAAGAAGCATTCATGGCCGTGTTGAGACTGGAAAAGGAGGTGCTATGAAAGT
upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 21
gtatatctctctataagggcgaaatcttgatttcatgattgt----atcttcagcggt-ttctgtgttccttaaaatgagtt-----tttgttttgaac-agGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAAGAAGCTTTCATGGCCGTTCTCAAACTTGAACGAGAAGTATTGTGACATC
| | || | || ||||||| | | ||||| ||| | | | | || || | ||| | | ||| | ||| |||| | ||| ||||| || ||||| | || |||| ||||||||| || ||||||||||||||||| ||| | ||||||||| || ||| | |||
-tttgcatcg-tggaaatgcgaaattatttatatgcaattgttttaatcctgattcataccttagattgctcataatagtattatcgtctgtctccaaccagGCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTTCCCCAAGAAGCTTTCATGGCAGTTTTGAAACTTGAAAAGGAGGTAATATGA----
upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 21
gtatatctctctataagggcgaaatcttgatttcatgattgtatcttcagcggtttctgt-----gttccttaaaatg-----agtttttgttttgaac-agGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAAGAAGCTTTCATGGCCGTTCTCAAACTTGAACGAGAAGTATTGTGACATC
| | || || || | ||||| | ||||| | | || | || || | ||| | | | ||| | ||| |||| | ||| ||||| || ||||| | || |||| ||||||||| || ||||||||||||||||| ||| | ||||||||| || ||| | |||
-tttgcatcg-tagaaatgtgaaattacttatatgcaattgttttaattctgattcatacctcagattgctcataatagtattattgtctgtctccaaccagGCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTGCCCCAAGAAGCTTTCATGGCAGTTTTGAAACTTGAAAAGGAGGTAATATGA----
upper sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 21
-----------------gtatatctctctataagggcgaaatcttgatttcatgattgtatcttcagcggtttctgtgttccttaaaatgagtttttgttttgaacagGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAAGAAGCTTTCATGGCCGTTCTCAAACTTGAACGAGAAGTATTGTGACATC
|| ||| | | ||| | |||| ||| |||| |||| | || || | || || | || | | ||||| | ||| ||||| |||||||| || || |||| ||||||||| |||||||| ||||||||||| || | ||||||||| || ||||| |||
gtaatgaattaatgtatgtttattttttattaaaagaaaaatgatgagaa-atga--aattctttccctgtgcatgactgttttctgatcatcttcttct-----cagGCTGAAGGAAAGAAAAGAATGAAGGCAATTGGTAAAGTTGATGTACCTCAAGAGGCTTTCATGGCTGTCTTGAAACTTGAAAAGGAGGTATTATGATTGTMapped 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|125311944|gb|EL326029.1|EL326029EST: TGTTATGGTGGAGATATTTCTCGGAAGAAGAAGCTTCTTAAGAAACAG GCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAA
genomic: TGTTATGGTGGAGATATTTCTCGGAAGAAGAAGCTTCTTAAGAAACAGgtatatctct ... ttttgaacagGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAA
EST:
gi|125104848|gb|EL158798.1|EL158798EST: GTGGAGATATTTCTCGGAAGAAGAAGCTTCTTAAGAAACAG GCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGA
genomic: GTGGAGATATTTCTCGGAAGAAGAAGCTTCTTAAGAAACAGgtatatctct ... ttttgaacagGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGA
EST:
gi|124914665|gb|EH988539.1|EH988539EST: GTGGAGATATTTCTCGGAAGAAGAAGCTTCTTAAGAAACAG GCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAG
genomic: GTGGAGATATTTCTCGGAAGAAGAAGCTTCTTAAGAAACAGgtatatctct ... ttttgaacagGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgtatcttcagcggtttctgtgttccttaaaatgagtttttgttttgaacagGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAAGAAGCTTTCATGGCCGTTCTCAAACTTGAACGAGAAGTATTGTGACATC
tttttgtttt CT-rich tract
ttaaaatgagttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatctctctataagggcgaaatcttgatttcatgattgtatcttcagcggtttctgtgttccttaaaatgagtttttgttttgaacagGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAAGAAGCTTTCATGGCCGTTCTCAAACTTGAACGAGAAGTATTGTGACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT