Sequence
atgc intronic sequence ATGC exonic sequence...gctacacggaatggaaaatgcttgtagatgctcatgattttctcatagattgtgcagctcctaacattgttgctgttgacttttggattttgttggctagGAATCTCTCTCAAGACTCAAGAGCTCTATGCGCTTGTGTTCTTGACTCGGTACTTGGATCTGTTTACGGATTATGTATCTCTGTACAACAGCATCATGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G29330.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G29330.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G29410.1 (Glycine max), 3'ss of exon 1
gctacacggaatggaaaatgcttgtagatgctcatgattttctcatagat-----tgtgcagctcctaacattgttgctgttgacttttggattttgttggctagGAATCTCTCTCAAGACTCAAGAGCTCTATGCGCTTGTGTTCTTGACTCGGTACTTGGATCTGTTTACGGATTATGTATCTCTGTACAACAGCATCATGAA
|| || | | | || | || | | ||| | | | |||| | |||| | | ||| || | ||| || |||| |||||||||||||||||| ||| |||||||| || | || || ||||||||||| ||||| | | || | ||||||| | |||||||
----tctcgagtgtcactccgtcactcacattcctccgccaaacaaaattccctatgtttgatttccatcatttcatcgattgattgtaactgtttattttc-agGGATTTCTCGCAAGACTCAAGAGCTCTACGCGATTGTGTTCGTGGCACGCTATTTGGATCTGTTCACGGACTTCATCTCCGTTTACAACACCTTCATGAA
upper sequence: AT1G29330.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G12570.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------gctacacggaatggaaaatgcttgtagatgctcatgattttctcatagat-----------tgtgcagctcctaacattgttgctgttgacttttggattttgttggctagGAATCTCTCTCAAGACTCAAGAGCTCTATGCGCTTGTGTTCTTGACTCGGTACTTGGATCTGTTTACGGATTATGTATCTCTGTACAACAGCATCATGAA
| | | || | | | |||| | || | | ||| | | | |||| || | | | || | || || ||| || |||| ||||||||||||||| || ||| |||||||| || | || || ||||||||||| ||||| | |||| | ||||||| | |||||||
gtctctctctcgcggttcccccaaaattggggctattttttattctatttttcaaatgttcattctcgagtgtcactcc-gtcactcacattcctccgccaaacaaaatttcctatgtttgatttccatcatt-ttaccgattgtttggaactgttatttttcagGGATTTCTCGCAAGACTCAAGAGCTGTACGCGATTGTGTTCGTGGCACGCTATTTGGATCTGTTCACGGACTTCATATCCGTTTACAACACCTTCATGAA
upper sequence: AT1G29330.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 1
gctaca-cggaatggaaaatgcttgtagatgctcatgattttctcatagattgtgcagctcctaacattgttgctgttgacttttggattttgttggctagGAATCTCTCTCAAGACTCAAGAGCTCTATGCGCTTGTGTTCTTGACTCGGTACTTGGATCTGTTTACGGATTATGTATCTCTGTACAACAGCATCATGAA
| || | || ||| || || || | || | | || | || | || ||| || | | | |||| || || ||||||||||| |||||||| ||||||||||| |||||||||| ||||||||||| ||||| | | || | || |||| | |||||
-cagcaaccaaagggagcattagggtttcccgtcgagtcatttctagggtttctttgaagtgaaaaactgagttcgtttgacattttctcctccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGTATTTGGATCTGTTCACGGACTTCATCTCAGTCTATAACACTGTGATGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagattgtgcagctcctaacattgttgctgttgacttttggattttgttggctagGAATCTCTCTCAAGACTCAAGAGCTCTATGCGCTTGTGTTCTTGACTCGGTACTTGGATCTGTTTACGGATTATGTATCTCTGTACAACAGCATCATGAA
ttttgtt CT-rich tract
attttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctacacggaatggaaaatgcttgtagatgctcatgattttctcatagattgtgcagctcctaacattgttgctgttgacttttggattttgttggctagGAATCTCTCTCAAGACTCAAGAGCTCTATGCGCTTGTGTTCTTGACTCGGTACTTGGATCTGTTTACGGATTATGTATCTCTGTACAACAGCATCATGAA
- - - - - - -gaaaatg