Sequence
atgc intronic sequence ATGC exonic sequence...tctttattgctttgacttataccaaattcagattctgcaaacaaaaaaacttctttgctcatacatacattaatcttctttctttcttttgattttgtagTTATAGAGCATTTGATGAATATGAAGGCATAGAAGTAGCATGGAACCAAGTTAAGCTATATGATTTCCTACAAAGCCCTGAGGATCTTGAGAGGCTTTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04910.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G30210.1 (Glycine max), 3'ss of exon 2
------tctttattgctttgacttataccaaattcagattctgcaaacaaaaaaacttctttgctcatacatacattaatcttctttctttcttttgattttgtagTTATAGAGCATTTGATGAATATGAAGGCATAGAAGTAGCATGGAACCAAGTTAAGCTATATGATTTCCTACAAAGCCCTGAGGATCTTGAGAGGCTTTAC
||| ||| ||| | || | | | | | ||| || ||| | | | | || | ||||| || ||| | || ||||||||||| ||||| ||| |||| || ||||| || |||||||| || ||| | ||||||||||| ||||||||||| ||||||||||||||||||
tgagtttctgtatgtttttctttcattttgtagaaaagggcatctgataaatttgattttttttttttgtgtgtgt-gatttgggttcttaatt--gat---gcagATATAGAGCATTCGATGAGTATCAAGGGATTGAAGTTGCTTGGAACCAGGTCAAGTTGTATGATTTCCTGCAAAGCCCTGAAGATCTTGAGAGGCTTTAC
upper sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G37180.1 (Glycine max), 3'ss of exon 2
tctttattgctttgacttataccaaattcagattctgcaaacaaaaaaacttctttgctcatacatacattaatcttctttcttt---cttttgattt-tgtagTTATAGAGCATTTGATGAATATGAAGGCATAGAAGTAGCATGGAACCAAGTTAAGCTATATGATTTCCTACAAAGCCCTGAGGATCTTGAGAGGCTTTAC
|||| || ||| | || | || | | || | | | | | | || | || | || | || ||| || || ||||||||||| ||||| ||| |||| || ||||| || |||||||| || ||| | ||||||||||| ||||||||||| |||||||| |||||||||
----aattgagtttctctatgtttttctttgagtttgtagaaaagggtatctgataatttttttttttttttttttttgtggcttgggttcttaattgatgcagATATAGAGCATTCGATGAGTATCAAGGGATTGAAGTTGCTTGGAACCAGGTCAAGTTGTATGATTTCCTGCAAAGCCCTGAAGATCTTGAAAGGCTTTAC
upper sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G43210.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------tctttattgctttgacttata--ccaaattcagattctgcaaa-caaaaaaacttcttt------gctcata--------catacattaatcttctttcttt--cttttgattttg-------tagTTATAGAGCATTTGATGAATATGAAGGCATAGAAGTAGCATGGAACCAAGTTAAGCTATATGATTTCCTACAAAGCCCTGAGGATCTTGAGAGGCTTTAC
| | ||| || | | || | ||| |||| | |||| | | | | ||| | | || ||| || |||| ||| ||| |||| || || || ||||||||||||||||| || |||| || ||||| || ||||| || ||||| | |||||||| || || |||||||| ||||| ||||||||||||
gtatgaatatttcagacaaatccctttccttatctttctcaatttcccgttttctttttgtttgtttcggttgattacgttactggccccacttctgattatacaaagctgagggtcctttttttctgagtttgtagaaatgggcatttgatattcttttttttttaatttttatttctgattggttcagATATAGAGCATTTGATGAGTACCAAGGGATTGAAGTTGCTTGGAATCAGGTTAAATTGTATGATTTTCTGCAGAGCCCTGAAGATCTCGAGAGGCTTTAC
upper sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0030g01660.t01 (Vitis vinifera), 3'ss of exon 2
--tctttattgctttgacttataccaaattcagattctgcaaacaaaaaaacttctttgctcatacatacattaatcttctttctttcttttgattttgtagTTATAGAGCATTTGATGAATATGAAGGCATAGAAGTAGCATGGAACCAAGTTAAGCTATATGATTTCCTACAAAGCCCTGAGGATCTTGAGAGGCTTTAC
|| |||||| |||| | || | |||| || | | | || | | | | ||| | | || || ||||| |||||||| ||||| ||||||||||| ||||| || |||||||| || ||||| ||||||||||| ||||||||||| |||||||||||||| |||
caaaatttgagctttgtgggtcttcaaaaagactttttccaaatgggt--ttttggtggatttgtgattgactggttgtttttttatgcttgatcggtgcagTTACAGAGCATTCGATGAGTATGAAGGCATTGAAGTTGCTTGGAACCAGGTCAAGCTTTATGATTTCCTGCAAAGCCCTGAAGATCTTGAGAGGCTCTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaacttctttgctcatacatacattaatcttctttctttcttttgattttgtagTTATAGAGCATTTGATGAATATGAAGGCATAGAAGTAGCATGGAACCAAGTTAAGCTATATGATTTCCTACAAAGCCCTGAGGATCTTGAGAGGCTTTAC
ttaatcttctttcttt CT-rich tract
atacatacattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctttattgctttgacttataccaaattcagattctgcaaacaaaaaaacttctttgctcatacatacattaatcttctttctttcttttgattttgtagTTATAGAGCATTTGATGAATATGAAGGCATAGAAGTAGCATGGAACCAAGTTAAGCTATATGATTTCCTACAAAGCCCTGAGGATCTTGAGAGGCTTTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG