Sequence
atgc intronic sequence ATGC exonic sequence...ttcttgctcaagatagcttggttataatccttgtgactggttaatgagtagttctgattctagtagtgatattatgttaaattaatcactttcttcatagGGGAGTGTCCTAGCTGGAAGAAGTGTTGTAGATGAATCTATGCTGACAGGAGAGTCACTTCCGGTGTTTAAAGAAGAAGGCTGCTCAGTTTCAGCGGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G21930.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G21930.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 4
ttcttgctcaagatagcttggttataatccttgtgactggtt--aatgagta--gttctgattctagtagtgatattatgttaaattaatcactttcttcatagGGGAGTGTCCTAGCTGGAAGAAGTGTTGTAGATGAATCTATGCTGACAGGAGAGTCACTTCCGGTGTTTAAAGAAGAAGGCTGCTCAGTTTCAGCGGGAA
|| | || | | || || || | | | |||| | || || ||| | || | || | ||| | || | || | | |||| | ||| | | ||||||||||||||||||||||| ||||| ||||| || |||||||| || ||||| || ||||| | ||||||||| || |
---ttaaaattggaggcctcccttaaagatttaagatggaatgtattgagaaacgtgttggttcatatggtattgcta-gctaactaaagaaattcatgaacagGGAATGGTCATTTCAGGAAGAAGTGTTGTAGATGAATCCATGCTTACAGGGGAATCACTTCCTGTATTTAAGGAGAAAGGCCTCACAGTTTCAGAAGGGA
upper sequence: AT5G21930.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 6
ttcttgctcaagatagcttggttataatccttgtgactggttaatgagtagttc--tgattctagtagtgatattatgttaaattaatcactttcttcatagGGGAGTGTCCTAGCTGGAAGAAGTGTTGTAGATGAATCTATGCTGACAGGAGAGTCACTTCCGGTGTTTAAAGAAGAAGGCTGCTCAGTTTCAGCGGGAA
|| | || | | || || | || |||| | | || ||| | | | || | ||| | | | || | |||| | ||| | | |||||||||||| |||||||||| ||||| ||||| || |||||||| || ||||| || |||| | |||||||||| ||||
ttaaaattggaggcttccct-tcatgatttaagatggaatgtattgagaaacttgttggttcatatgatattgcta-gctaactagaaaaattcatgagcagGGAACGGTCATTTCAGGAAGAAGTGTTATAGATGAATCCATGCTTACAGGGGAATCACTTCCTGTATTTAAGGAGAAAGGGCTCACAGTTTCAGCAGGAA
upper sequence: AT5G21930.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 6
ttcttgctcaagatagcttggttataatccttg--tgactggtta-atgagtagttctgattctagtagtga-tattatgttaaattaatcactttcttcatagGGGAGTGTCCTAGCTGGAAGAAGTGTTGTAGATGAATCTATGCTGACAGGAGAGTCACTTCCGGTGTTTAAAGAAGAAGGCTGCTCAGTTTCAGCGGGAA
||| | | | | || || || | ||| || | | | |||| | || | | ||| ||||| | ||||| | | | || | |||| || || || ||||||||||||||||| || || || ||||| |||||||| |||||||| || ||||| ||||| || | || || || ||||
--attggtgatg-tggcatgagaatctttctttcctgtttagacatatgaaatttggtggtctccatgttgaatattagctgaaattgaa-agtgcctatacagGGAAGAGTTCTTGCTGGAAGAAGTGTTGTGGACGAGTCCATGCTTACAGGAGAATCACTTCCTGTATTTAAGGAAGAGGGTTTTGTGGTCTCTGCTGGAAMapped 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|164197927|gb|EL987174.1|EL987174EST: GCCTGGTGAGACATTTCCTGTCGAT GGGAGTGTCCTAGCTGGAAGAAGTGTTGTAGATGAATCTATGCTGACAGGA
genomic: GCCTGGTGAGACATTTCCTGTCGATgtaagtgttt ... ttcttcatagGGGAGTGTCCTAGCTGGAAGAAGTGTTGTAGATGAATCTATGCTGACAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtagttctgattctagtagtgatattatgttaaattaatcactttcttcatagGGGAGTGTCCTAGCTGGAAGAAGTGTTGTAGATGAATCTATGCTGACAGGAGAGTCACTTCCGGTGTTTAAAGAAGAAGGCTGCTCAGTTTCAGCGGGAA
aattaat putative branch site (score: 3)
tcactttcttc CT-rich tract
atattatgttaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcttgctcaagatagcttggttataatccttgtgactggttaatgagtagttctgattctagtagtgatattatgttaaattaatcactttcttcatagGGGAGTGTCCTAGCTGGAAGAAGTGTTGTAGATGAATCTATGCTGACAGGAGAGTCACTTCCGGTGTTTAAAGAAGAAGGCTGCTCAGTTTCAGCGGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - caagata
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc