Sequence
atgc intronic sequence ATGC exonic sequence...atcatgtttatcatcaacgtttttgttgcatttggtgtctgatgggatatagatgatgtgagattcttatctgattttttctagtgtcacccattttcagCTGCATTTGGAGCAGTCCTACATGTTATATCCACTTCTCTCCTTGGTATAACAGCAATCACAATGGCGAATACCATCGCTGGTGAAGAGACTGTTCACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G21070.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G21070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G44180.1 (Glycine max), 3'ss of exon 1
-atcatgt-ttatcatcaacgtttttgttgcatttggtgtctgatgggatatagatgatgtgagattcttatctgattttttctagtgtcacccattttcagCTGCATTTGGAGCAGTCCTACATGTTATATCCACTTCTCTCCTTGGTATAACAGCAATCACAATGGCGAATACCATCGCTGGTGAAGAGACTGTTCACAA
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aactacaaaccaagctcgataaattctttgtacctgtcctcattgccattgaaagctctttgaatttcctacttaaccttattcattttatttcatg--cagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAACAGCAATTACCATGGCAAACACCATTGCTGGTGAAGAAACAGTGCATAA
upper sequence: AT5G21070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G04600.1 (Glycine max), 3'ss of exon 1
atcatgtttatcatcaacgtttttgttgcatttggtgtctga--tgggatatagatgatgtgagattcttatc-tgattttttctagtgtcacccatttt--------cagCTGCATTTGGAGCAGTCCTACATGTTATATCCACTTCTCTCCTTGGTATAACAGCAATCACAATGGCGAATACCATCGCTGGTGAAGAGACTGTTCACAA
| | | | | | ||| | || || | | ||||||| || | | |||| || | | |||||| ||||||| |||||||| | | || || ||||||||||| || ||||||||||| ||||| || ||||| || ||||| ||||||||||| ||||| || ||
-----------cccttattcccatatgatgtctagtgcaaagactcagaagactgtgttctcagattctgttcataaagttttttaaccttattcattttatttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAACGGCAATTACCATGGCAAACACCATTGCTGGTGAAGAAACTGTGCATAA
upper sequence: AT5G21070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0009g01580.t01 (Vitis vinifera), 3'ss of exon 1
atcatgtttatcatcaacgtttttgttgcatttggtgtctga--tgggatatagatgatgtgagattcttatctgattttttctagtgtcacccatttt----cagCTGCATTTGGAGCAGTCCTACATGTTATATCCACTTCTCTCCTTGGTATAACAGCAATCACAATGGCGAATACCATCGCTGGTGAAGAGACTGTTCACAA
| | |||| | | | | | || || | | || || || | | ||| || |||| | | | ||||| |||||||||||||||| | | ||||| ||||||||||| || |||||| | ||||||||||| ||||| || | || ||||| || || || || || ||
----ttcaactgctcaatctcgatatgaaaatcggccagggaattctgctaagaatagtgcttgttgttta--caatctttttaacagctatttatttttatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCACAGCAATCACCATGGCAAACAGTATTGCTGGGGAGGAAACAGTCCATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatagatgatgtgagattcttatctgattttttctagtgtcacccattttcagCTGCATTTGGAGCAGTCCTACATGTTATATCCACTTCTCTCCTTGGTATAACAGCAATCACAATGGCGAATACCATCGCTGGTGAAGAGACTGTTCACAA
atctgat putative branch site (score: 4)
cccattttc putative PPT
ttatctgatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcatgtttatcatcaacgtttttgttgcatttggtgtctgatgggatatagatgatgtgagattcttatctgattttttctagtgtcacccattttcagCTGCATTTGGAGCAGTCCTACATGTTATATCCACTTCTCTCCTTGGTATAACAGCAATCACAATGGCGAATACCATCGCTGGTGAAGAGACTGTTCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - -catcaac
- - - - - - - - - gtttttg