Sequence
atgc intronic sequence ATGC exonic sequence...atatctgaaaccccattttctagttgtctatctgtagtgaagatgttctgtagcaaaattgcgcttcctcatataccgttttctctttgatctttttcagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTTGATGCCAAAACATTCGTTGAAGAAGACACATTCATGACAGATGAACCCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G61150.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g38970.1 (Oryza sativa), 3'ss of exon 4
------atatctgaaaccccattttctagttgtctatctgtagtgaagatgttctgtagcaaaat-tgcgcttcctcatataccgttttctctttgatctttttcagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTTGATGCCAAAACATTCGTTGAAGAAGACACATTCATGACAGATGAACCCG
|| | || || || | || || ||| | | | | || ||| | | | || | | ||| | | | | | | ||| | ||||||| |||| || || || ||||| ||||||||||| ||||||||||||||| | ||||||| || || || || ||| | ||||||||| | |
taggctttactaggaatgttatgatcga--tgcttaaatgtttttgtgct--tttgcagctattcatatggttatttgt-tactgactaatttcttaacttgt--agATGAATGTGATCAAGGTATCAAATATTATGGGGATTGACCCAAAGCCTTTTGATCCTAAAACATATGTGGAGGAGGATGTATTTGTTACAGATGAATCTG
upper sequence: AT5G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 4
atatctgaaaccccattttctagttgtctatctgtagtgaagatgttctgtagcaaaat-tgcgcttcctcatat----accgttttctctttgatctttttcagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTTGATGCCAAAACATTCGTTGAAGAAGACACATTCATGACAGATGAACCCG
| | |||| || | | | | | ||||| | || | ||| | | | ||||||| | ||| ||| | | |||||||||||||| |||||||||||||| ||||| |||||||||| || |||||| | ||||||| || ||||| || || || | || |||||| | |
-----aaatgttgccttttgtaatgatgtgcattctggtaagatatgttgaatttcaatattcaactactcatattttaaatttttaatctctctctcatggcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCCTTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACTGATGAATCTG
upper sequence: AT5G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G21900.2 (Glycine max), 3'ss of exon 4
--atatctgaaaccccattttctagttgtctatctgtagtgaagatgttctg-tagcaaaattgcgcttcctcatataccgttttctctttgatctttttcagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTTGATGCCAAAACATTCGTTGAAGAAGACACATTCATGACAGATGAACCCG
| | | |||| || ||| | | | || ||| || ||| | | | | | | ||||| | || |||||||||||||| |||||||||||||| ||||| |||||||||| || |||||| | ||||||| || ||||| || || || | || |||||| | |
ccctttgtactgatgtgcattctggtaagatatgttgaatttcaatattcaactactcgtattttaaattttta---atctctctctctctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG
upper sequence: AT5G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g07160.t01 (Vitis vinifera), 3'ss of exon 4
atatctgaaaccccattttctagttgtctatctgtagtgaagatgttctg---tagcaaaattgcgcttcctcata--taccgttttctctttgatcttttt-cagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTTGATGCCAAAACATTCGTTGAAGAAGACACATTCATGACAGATGAACCCG
|| ||| | ||| | ||||| | | || | ||| ||| || | | | ||| | | || || ||||||||||||||||||||||| ||||| ||||| ||||| |||||||| ||||| | ||||| | ||| ||||| |||||||| ||||||||||| | |
------ctaatagtgccttcagatcatctgatacttgtgaaagtctatcaatttatctgtcttgagctgtggcaaaattttaatattcaatagtactttgttacagATGAACATGATAAAAGTTTCTAATATAATGGGCATTGAACCAAAGCCATTTGACCCTAAAACGTACGTAGAAGAGGACACATTTGTGACAGATGAATCTGMapped 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|116415234|gb|EG457826.1|EG457826EST: CTTTGGAAGTGGAGGTTCCTTTCCGCCCTCCTCCAGGTGACCCCGTTAAG ATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTT
genomic: CTTTGGAAGTGGAGGTTCCTTTCCGCCCTCCTCCAGGTGACCCCGTTAAGgtatacctgc ... tctttttcagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTT
EST:
gi|116415235|gb|EG457827.1|EG457827EST: CTTTGGAAGTGGAGGTTCCTTTCCGCCCTCCTCCAGGTGACCCCGTTAAG ATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTT
genomic: CTTTGGAAGTGGAGGTTCCTTTCCGCCCTCCTCCAGGTGACCCCGTTAAGgtatacctgc ... tctttttcagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgtagcaaaattgcgcttcctcatataccgttttctctttgatctttttcagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTTGATGCCAAAACATTCGTTGAAGAAGACACATTCATGACAGATGAACCCG
ctttgat putative branch site (score: 5)
ccgttttctctttgat CT-rich tract
atcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatctgaaaccccattttctagttgtctatctgtagtgaagatgttctgtagcaaaattgcgcttcctcatataccgttttctctttgatctttttcagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTTGATGCCAAAACATTCGTTGAAGAAGACACATTCATGACAGATGAACCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG