Sequence
atgc intronic sequence ATGC exonic sequencegtatcataatgtgaattggatttgtctttcttgtcctgacactgctcttttatatttgattggaatttcaacgatggcaatcttaaatcttgcagTGTGATTTATTGGACTTGCCAGCCGTAGCACAATTGGAAAAGGATGCTAAATATGCACCTGTTTACCAACTTCTGAAGATTTTTCTTACTCAGAGGTTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G02200.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G02200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G28080.2 (Glycine max), 3'ss of exon 4
--gtatcata-atgtgaattggatttgtct--ttcttgtcctgac-actgctcttttatatttgattggaatttcaacgatggcaatcttaaatcttgcagTGTGATTTATTGGACTTGCCAGCCGTAGCACAATTGGAAAAGGATGCTAAATATGCACCTGTTTACCAACTTCTGAAGATTTTTCTTACTCAGAGGTTAA
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tactcttatatatctaaatccaatatttttaattccatttttggctaagattgttgtaagttcttgaagagttttcaatatgttgattgttg-tgttttagTGTGATTTGCTAGACTTGCCTGCTGTTGCACAACTGGAGAAGGATGCCAAATATGCTCTGTTATATCAGCTTCTTAAGATTTTTCTTACCCAGAGGCTGG
upper sequence: AT3G02200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G22090.1 (Glycine max), 3'ss of exon 5
-------gtatcataatgtgaattggatttgtctttcttgtcctgacactgctcttttatatttgattggaatttcaacgatggcaatcttaaatcttgcagTGTGATTTATTGGACTTGCCAGCCGTAGCACAATTGGAAAAGGATGCTAAATATGCACCTGTTTACCAACTTCTGAAGATTTTTCTTACTCAGAGGTTAA
|||| | || | | ||| | || ||| | || | | || || || | || | | || | | ||| ||||||||||| | |||||||| || || ||||| |||| |||||||| |||||||| | | || || ||||| |||||||||||||| |||||| |
aactcttgtatatctaagtccaatacttttaa-tgtcatgtttggccaagattgtagtaagttcttgaagagcattcactaagttgattgttg-tgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAATATGCTCTGTTATATCAGCTTCTTAAGATTTTTCTTACCCAGAGGCTGG
upper sequence: AT3G02200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 5
-gtatcataatgtgaattggatttgtctttctt--gtcctgacactgctcttttat-atttgattggaatttcaacgatggcaatcttaa--atcttgcagTGTGATTTATTGGACTTGCCAGCCGTAGCACAATTGGAAAAGGATGCTAAATATGCACCTGTTTACCAACTTCTGAAGATTTTTCTTACTCAGAGGTTAA
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tgcaccacc-tgttattctctttattttttcttcagtcttgattataattttgggttgggtgcccagaaaattaattcctttttttttggttgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAATATGCATTGGTCTATCAGCTTCTGAAGATTTTTCTCACTCAGAGGCTTGMapped 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|86045217|gb|DR340972.1|DR340972EST: AGGCTGTGCGTGCAGTTATCGAATTTGTCAAAGCTTCCAGTATTTTCCAG TGTGATTTATTGGACTTGCCAGCCGTAGCACAATTGGAAAAGGATGCTAAA
genomic: AGGCTGTGCGTGCAGTTATCGAATTTGTCAAAGCTTCCAGTATTTTCCAGgtatcataat ... aatcttgcagTGTGATTTATTGGACTTGCCAGCCGTAGCACAATTGGAAAAGGATGCTAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgctcttttatatttgattggaatttcaacgatggcaatcttaaatcttgcagTGTGATTTATTGGACTTGCCAGCCGTAGCACAATTGGAAAAGGATGCTAAATATGCACCTGTTTACCAACTTCTGAAGATTTTTCTTACTCAGAGGTTAA
atttgat putative branch site (score: 5)
ttttatatttgattgg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcataatgtgaattggatttgtctttcttgtcctgacactgctcttttatatttgattggaatttcaacgatggcaatcttaaatcttgcagTGTGATTTATTGGACTTGCCAGCCGTAGCACAATTGGAAAAGGATGCTAAATATGCACCTGTTTACCAACTTCTGAAGATTTTTCTTACTCAGAGGTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA