Sequence
atgc intronic sequence ATGC exonic sequence...ataaccttattgataaaaatcaggtcagagtatgggcttgggcgatctgtaaacattacttggctttaatggtggctaatatctttttgttgtgcatcagATTCGTGTGAGGACATGTTAATCGAGAACTCTTACATCAGCGTTGGGGATGATGGAATCGCAATAAAGAGCGGTTGGGACCAGTATGGAACTACATATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G42950.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g26800.1 (Oryza sativa), 3'ss of exon 3
-ataaccttattgataaaaatcaggtcagagtatgggcttgggcgatct-gtaaacattacttggctttaatggtggctaatatctttttgttgtgcat-cagATTCGTGTGAGGACATGTTAATCGAGAACTCTTACATCAGCGTTGGGGATGATGGAATCGCAATAAAGAGCGGTTGGGACCAGTATGGAACTACATATGG
| |||| | | | |||| || |||| ||| || | |||||| ||| | || | || |||| | | || ||||||| |||||| | | | || | |||| || || ||||| |||||||| || || |||||||| ||||||||||| ||||||| | | |||||
gacaaccctgtattcctacatcatgttggagtc---atttgtattatttagtaaactttatgcttcactagtaagattctcaattattttactatatatgcagATTCTTGTGAGAATGTAGTGATTAAAAACTGCTATATTTCTGTTGGTGATGATGGGATTGCTATAAAGAGTGGTTGGGACCAATATGGAATTGCTTATGG
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G135763_T01 (Zea mays), 3'ss of exon 3
ataaccttattgataaaaatcaggtcagagtatgggcttgggcgatctgtaaacattacttggctttaat-ggtggctaatatctttttgttgtgcat-cagATTCGTGTGAGGACATGTTAATCGAGAACTCTTACATCAGCGTTGGGGATGATGGAATCGCAATAAAGAGCGGTTGGGACCAGTATGGAACTACATATGG
| || | | | || || | | || | | ||| ||| | ||||| | | | || ||| ||| || ||||||| ||||| | || | || | |||| ||||| ||||| |||||||| || || |||||||| ||||||||||| ||||||| | | |||||
agaaacctgcactgcatgtccatgttctcttgaagcctctttt--ttttaaaagtttatgcttcattaatcaatctgtttgttattcttgatgtatatgcagATTCTTGTGAAAATGTGGTGATAAAAAACTGCTACATTTCTGTTGGTGATGATGGGATAGCCATAAAGAGTGGTTGGGACCAATATGGAATTGCTTATGG
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 3
ataaccttattgataaaaatcaggtcagagtatgggcttgggcgatc-tgtaaacattacttggctttaatggtggctaatatctttttgttgtgcat-cagATTCGTGTGAGGACATGTTAATCGAGAACTCTTACATCAGCGTTGGGGATGATGGAATCGCAATAAAGAGCGGTTGGGACCAGTATGGAACTACATATGG
| | || || || | ||| || || | || | || | | | | || || | ||| ||| | ||||||| |||||||| ||| | || || ||| ||| || || ||||| ||||||||||| ||||||||||| |||||||| ||||||||| | | |||||
gcatttgccctagtactt-ccaagttcatgaatgtttttccttaattatttatattatattcagtatcagtgact-tcaaccaatctttattgcataaacagATTCATGTGAGGATATGGTGATTGAAGACTGTTATATTAGTGTTGGAGATGATGGAATTGCAATAAAGAGTGGTTGGGATCAGTATGGAGTTGCCTATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtaaacattacttggctttaatggtggctaatatctttttgttgtgcatcagATTCGTGTGAGGACATGTTAATCGAGAACTCTTACATCAGCGTTGGGGATGATGGAATCGCAATAAAGAGCGGTTGGGACCAGTATGGAACTACATATGG
ggctaat putative branch site (score: 3)
tctttttgtt CT-rich tract
taatatctttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaccttattgataaaaatcaggtcagagtatgggcttgggcgatctgtaaacattacttggctttaatggtggctaatatctttttgttgtgcatcagATTCGTGTGAGGACATGTTAATCGAGAACTCTTACATCAGCGTTGGGGATGATGGAATCGCAATAAAGAGCGGTTGGGACCAGTATGGAACTACATATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- aacctta
- - - - - - ataaaaa
- - - - - - - - - - - - - - - - - ggcttgg
- - - - - - - - - - - - - - - - - - - - - - - - gtaaaca