Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctctatatcttcttcgacaacttcgttttaagtccatatggtgagagtatgtcatgaatttgcttatcgttttttggaatggaagTCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35920.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 2
-------gtaagtc--tctatatcttcttcgacaacttcgttttaagtccatatggtgagagt-----atgtcatgaatttgcttatcgttttttggaatggaagTCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAG
|| || | || ||| ||| | || ||| | | ||| | | |||| | || || | | |||| | || ||| |||||| ||||||||| | ||||| | ||||||||||| |||| ||||||||||| || |||||||| | |||||||| || || |
gtatataatagatcatttgatgcctttttccgtatctctaacttacacttggaggctgacaaattccattttcattatcctgtttttaacctgggggaa-gATAGCAATGTGTACAACAAAGGGAAGACAATTGTTTTCAGCAAAGTTCCACTACCTGATTATCGAGCAGACCTTGATGAGAGACATGGATCAACACAACA----
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 4
--gtaagtctctatatcttcttcgacaacttcgttttaagtccat--atggtgagagtatgtcatgaatttgcttatcgtttttt-----ggaatggaagTCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAG
| | ||| || || || | | | | | | ||| | | | | | || || | ||||| || | | ||| |||| ||||| ||||||||| | |||||| | ||||| || || ||||| ||||||||||| ||||| || || |||||||||| || || || |||
tttcaccatttgatacctactgttttgcctatgaaccatactcttcaaagctgacaaattctactttacctggtttgcatttttaacgtggggaagatagTAATGCATACAACAAAGGGAAGACACTTGTTTTCAGCAAGGTACCCTTACCTGATTATCGAGCAGATCTGGACGACAGGCATGGATCAACACAAAAGGAG
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 4
---------gtaagtctctatatcttcttcgacaacttcgttttaagtccatatggtgag-agtatgtcatgaatttgcttatcgttttttgg-aatggaagTCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAG
|| | | || | | | ||| | ||| | ||| | | | || | | ||| || || || || || | ||| ||||| || | ||| ||||||| ||| |||||||||||||||| || || |||||||| || ||||||||||| || |||||||| || |||||||||
aagcatagattacctgtactgatgaacattttgagcttaatcttatttttttattttaactaacatcttaatggcttgatt--tgtacttgggcaaagaaagCCATGCTTATAGTAAGGGGAAGGTTCTCATTGTTAGCAAAGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAAGAG
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtctctatatctt-cttcgacaacttcgttttaagtccatatggtgagagtatgtc--atgaatttgcttatcgttttt-------tggaatggaagTCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAG
| | | | | || || || | | || | |||||| || || || | |||| ||| | | |||| ||||| | ||| ||||| || || || |||||| | |||||||| ||||||||||| || ||| |||| || || |||||||||||||| ||||||||||| || ||||||
-catattcatgtctgttgttttgatggtacccctgtagttgtctatggttagcctaaatcttacaaattctcttcttgattttgtgcttgtggaaagaaagCCATGCATATAACAAGGGGAAGACACTTGTTGTCAGCAAAGTTCCATTGCCAAATTACCGGGCTGATCTTGATGAACGCCATGGATCCACACAAAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtccatatggtgagagtatgtcatgaatttgcttatcgttttttggaatggaagTCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAG
ttttttg CT-rich tract
atgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctctatatcttcttcgacaacttcgttttaagtccatatggtgagagtatgtcatgaatttgcttatcgttttttggaatggaagTCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA