Sequence
atgc intronic sequence ATGC exonic sequencegtataatgttgtttaatcaaatcttttgactgacgctgattatgtttagtgatcctagtatggacaataacatctattattgcttgccagATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G26990.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
gta-taatgttgtttaatcaaatcttttgactgacgctgattatgtttagtgatcctagtatggacaataacatctattattgcttgcc--agATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGA
|| | || || || | || ||| | | | || || | || | | || | | | ||| | |||| |||||||| || ||||| |||||||||| |||||||| ||||||||||||||||||| | || || | || || ||||| ||||| || || |
gtgcttatacaagtttctctagtcaattggttttcttta--catattctgcagtcattactctaattattttgctcgtaacttcttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
upper sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 5
------------gtat-aatgttgtttaatcaaatcttttgactgacgctgattatgtttagtgatcctagtatg-gacaataacatctattattgcttgcc-agATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGA
|| | |||| | || || ||| | | | ||| || | ||| | | | |||| || | || | || | | || |||| ||||||| || || || |||||||||||||||||||| || ||||| |||||||| || | |||||||| || |||||||| |||||||||||||
actccttggtatacatcagtgttatgtagaataacttttatagttgcactg--catcgtcagt-agcatcatatgtgatgctgac--caatggtcgtgtgtttagATCTTGAAGGAGCTTCACAAATCTTGTCAAAAGGAAGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGA
upper sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------gtataatgttgtttaatcaaat--------cttttgactgacgctgattatgtttagtga--tcctagtatggacaa------taacatcta----ttattgcttgc-cagATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGA
| || || | ||||| || | ||||| | | | |||| |||| | |||| || || || | | | | || | | | |||||| ||||||| |||||||| |||||||| ||||||||||| || ||||| |||||||| || | || |||| ||||| ||||| || || |||||||
gtaagtattctgcccgttgactcctcaactttattttcatatctttcaactttatctagtattgaatgatttcgtttactcggaataccagtacttttcaaaatgggatgtaatgtgtagtaaattccttgttctgagaaaacttgtgatactcacagcttgtcgtacgtgcagATTTTGAAGGAGCTCCATAAATCTTGTCAGAAGGAAGATGGTACAGATGACCAGAAGAAGGGCACACAATTGCTGGAGGTGTATGCGATAGAGATTCAGA
upper sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------gtataatgttgtttaatcaaatcttttgactgacgctgattatgtttagtgatcctagtatggacaataacatctattattgcttgc--cagATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGA
|||| | || | | | | | | ||| || ||| ||| | | | ||| || ||| | | |||||| ||||||| ||||| || |||||||| || |||||||| || |||||||||||||| || | || |||| ||||||||||| || || |||||||
gtaagttcgctgccagttgatttctccacaatatcttcatatgtcctattttatctgataataaatgtcagtcgcttatctcaatgcttttcagttcgagatatatgtt--cgcagaatatattttttcgtacacaaatgtgagatgcttctaatttcttagaactgcagATTTTGAAGGAGCTCCACAAATCTTGTCAGAAAGAAGATGGTACAGATGATCAGAAGAAGGGCACACAATTGCTCGAGGTTTATGCGATAGAGATTCAGA
upper sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ29478 (Selaginella moellendorffii), 3'ss of exon 5
gtataatgttgtttaatcaaatcttttgactgacgctgattatgtttagtgatcctagtatggacaataacatctattattgcttgccagATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGA
| |||| | ||||| | | | | || | | ||| ||||| |||| || ||||| | || || || | |||||||| ||||||||||||||||||||| |||||| || || || || || ||||| |||||||
--------------------------------gtaat-attagcctgggtgattttttttaattttctggc-cctcctttcgctgcatagATTTTGAAAGAGCTCCACAGATCGTGCCAGAGAGAAGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGA
upper sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ28052 (Selaginella moellendorffii), 3'ss of exon 5
gtataatgttgtttaatcaaatcttttgactgacgctgattatgtttagtgatcctagtatggacaataacatctattattgcttgc-cagATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGA
| ||| | ||||| | || | | | | | ||| ||| ||||| |||| || ||||| | || || || | |||||||| ||||||||||||||||||||| |||||| || || || || || ||||| |||||||
--------------------------------gtaatc-ttagcctgggtgatttttcta---attttctgacccttcattctctgcatagATTTTGAAAGAGCTCCACAGATCGTGCCAGAGAGAAGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGAMapped 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|86049782|gb|DR345537.1|DR345537EST: AACTCTGCAACATCTGGTTTGACATTGGTGAATACAGACGGATGACTAAG ATTCTGAAGGAACTCCATAAGTCTTGNCCAAAGGAAGATGGAACTGGTGAT
genomic: AACTCTGCAACATCTGGTTTGACATTGGTGAATACAGACGGATGACTAAGgtataatgtt ... tgcttgccagATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgattatgtttagtgatcctagtatggacaataacatctattattgcttgccagATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGA
caataac putative branch site (score: 2)
aataacatctattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatgttgtttaatcaaatcttttgactgacgctgattatgtttagtgatcctagtatggacaataacatctattattgcttgccagATTCTGAAGGAACTCCATAAGTCTTGTCAAAAGGAAGATGGAACTGATGATCAGAAGAAAGGAAGTCAGCTGCTTGAGGTTTATGCAATTGAAATTCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT