Sequence
atgc intronic sequence ATGC exonic sequence...tctgtgaaagtttttcttacttgatatgtcttcctgggaatcttttatggattttaagctctatgttttgattttaacttcccattgtaattgtttccagGTTTATTGTTATTACCCTTTCTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G44340.2 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G44340.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA10G42720.1 (Glycine max), 3'ss of exon 16
-------tctgtgaaagtttttcttacttgatatgtcttcctgggaatcttttatggattttaagctctatgttttgattttaacttcccattgtaattgtttccagGTTTATTGTTATTACCCTTTCTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCA
|| | | | |||||||| | | |||| | ||| | | | || | || | | ||||||||| | | ||||||||| |||| ||||||||||||||||||||||| || | |||| | ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| |
aatattgcgcgttttaatctacaacacttgatacattcataccttcttttttt-tcaattatgtgttttacatattaaagt-aacttcccacttt-----tttccagGTCTATTACTATTACCCTTTCTCAGCTCTTTCTGATACTGCAAAACTTTACAATGATCTTAGATGGAACATCACTAGGCCACAAGGTTTTGAGGCTGTAA
upper sequence: AT3G44340.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA20G24330.1 (Glycine max), 3'ss of exon 16
-tctgtgaaagtttttcttacttgatatgtcttcctgggaatcttttatggattttaagctctatgttttg-attttaacttcccattgtaattgtttccagGTTTATTGTTATTACCCTTTCTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCA
|||| || |||| || | | | | | | | |||| | ||| || | | |||||| || |||| | | | | || ||||||||| |||| |||||||| |||||||||||||| || | |||| | ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| |
tgttgtgtgttttattct-acatcacttattacattcttactttttttttcctttcaa-ttatgtgttttacatattaaagtaacttctcacttttttccagGTCTATTACTATTACCCCTTCTCAGCTCTTTCTGATACTGCAAAACTTTACAATGATCTTAGATGGAACATCACTAGGCCACAAGGTTTTGAGGCTGTAA
upper sequence: AT3G44340.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv19s0014g05310.t01 (Vitis vinifera), 3'ss of exon 15
---tctgtgaaagtttttcttacttgatatgtcttcctgggaatcttttatggattttaagctctatgttttgattttaacttc--ccattgtaattgtttccagGTTTATTGTTATTACCCTTTCTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCA
| | || || | || | | ||| || | ||| | || || ||| | | || |||| | ||| | || ||||| |||| ||||||||| |||||||| ||||| || || | ||| | ||||| || ||||||||||| ||||| | |||||||||||||||||| || |
tcttttatggtcgtaaggttctattttcaagacttgct-----ccatttttagaacttgctctcaaaaataagaggttaatgcaaactgttgccctcactttcagGTGTATTATTATTACCCCTTCTCAGCCCTTTCTGATCCTGCTAAGCTTTACAATGACCTTAGATGGAACATCACAAAGCCCCAAGGTTTTGAGGCAGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatggattttaagctctatgttttgattttaacttcccattgtaattgtttccagGTTTATTGTTATTACCCTTTCTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCA
ttttaac putative branch site (score: 2)
ttgtttcc putative PPT
tatgttttgattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgtgaaagtttttcttacttgatatgtcttcctgggaatcttttatggattttaagctctatgttttgattttaacttcccattgtaattgtttccagGTTTATTGTTATTACCCTTTCTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg