Sequence
atgc intronic sequence ATGC exonic sequencegcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18040.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 2
---gcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
| | || | | ||||| || || |||||| || || || || |||| | | ||| ||| | || | |||| | ||| || ||||| ||| | ||||| || |||||||||||||| ||||||||||| ||||| ||||||| || || ||||| |||||||| |||||
gtagtagattccatatagtaggaaatcggtaatttcttttgcttatg--tggttgacacgctcactttc-tgg------tttctctttg---cagCAAGTGTTTTCCATCGGGATCTTAAGCCCAAGAATATTCTAGCCAATGCTGATTGCAAGCTGAAGGTTTGCGATTTCGGCCTTGCCCGAGTGTCATTTAA
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 2
---gcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
| || | | | | || | ||| | | ||||| ||| | | ||| | | | || || || | |||| | || || ||||| ||| | ||||| || |||||||||||||| |||| |||||| |||||||||| || ||||| ||||| || || || || ||
gttgttagactccacattgagtggacttgttaatggtttgttacgttacttcttgtgagcttcagtttc-tatgcttgttcttggttt--tgcagCAAGCGTCTTCCATCGGGATCTTAAGCCCAAGAATATTCTAGCCAATGCTGACTGCAAGCTGAAGATTTGTGATTTTGGCCTTGCCCGCGTTTCATTCAA
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 2
gcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
| || | | || | | || |||| | || | | | | | | || | |||| || ||||||||||||||||||||||| ||||||||||| || ||| |||||||||| | || || || || ||||||||||||||||| || |||||
--------------gtattgcatccttattataaccaggtccttgacttttttagatagagatattaaactagtgtatcatttttcttgcagCAAACGTGTTTCATCGTGATTTGAAGCCAAAAAATATTCTTGCTAACGCTGATTGCAAACTAAAAATATGTGATTTTGGGCTTGCTCGAGTTTCATTTAA
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 2
gcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
|| | | | | | | | | | | | | || | | | | || || | | | |||| | | |||| |||||||||||||||||||||||||| ||||| ||||| || ||| |||||||||| | || || || || ||||||||||||||||| || |||||
----gtattgtatccttattatgacaaggtccttccttgacttttttagatagtgatattaaactagtatatcatttttct------tgcagCAAATGTGTTTCATCGTGATTTGAAGCCAAAAAACATTCTTGCTAACGCTGATTGCAAACTAAAAATATGTGATTTTGGGCTTGCTCGAGTTTCATTTAA
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 2
gcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
|| | ||| || |||| | |||| | | | | | | | | |||| || || | |||| ||||||||||||||||| |||||||| |||||||||||||| || ||||||||||| | || | || || ||||| ||||||||||| || |||||
-------------------gtatccttgtaa--ttaagtccttgactgttgctgatagtgataataaactaaaataacattttttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 2
gcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
|| | ||| || |||| | |||| | | | | | | | |||| || ||| | |||| ||||||||||||||||| |||||||| |||||||||||||| || || ||||||| | || || || || || || ||||||||||| || |||||
-------------------gtatccttgtaa--ttaagtccttgactgttgcagatagtgatattaaactaaaataacattcttct-tgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTAATTGCAAACTAAAAATATGTGATTTCGGACTTGCTCGAGTTTCATTTAA
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0011g04920.t01 (Vitis vinifera), 3'ss of exon 2
gcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaact-tttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
| | |||| | || | | | || | | | || || | | | | |||||| || | | | |||||| | |||| |||||||||||| | ||||| ||||| ||||| || || || || | || ||||| |||||||||| || |||||||||||||| ||||| |||||
gttgg-acctttgtttaaaattgtgccattatcgtatttcttttg--gttctatattctcaatgaccaataatattgtctttattt--tgcagCAAATGTGTTTCATAGAGATTTAAAGCCAAAAAACATCCTTGCTAATGCAGACTGCAAACTGAAGATTTGTGATTTTGGGCTTGCTCGCGTGTCATTTAA
upper sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 2
gcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
| |||| || || | | | | || ||||| | | | || || || |||| ||| | || | |||| |||||||||||||| ||||||||||| ||||||||||| || || | || ||||||||||||||||| || |||||||||||||| ||||| || ||
gttggtgcttttcagagatattatagcctcaccgtttgtttgcttttatgtcctgaatggccactaata-aaaattttatggtttcttccagCAAATGTGTTTCATCGAGATTTGAAGCCAAAAAATATTCTTGCTAATGCCGACTGCAAGTTGAAGATTTGTGATTTTGGGCTTGCTCGGGTGTCATTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
atctgat putative branch site (score: 4)
cttttttattc putative PPT
aaaacttttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcgagtgccttggcttgagaaattcgtgtttccttttgtccattactgcttttcaaactcaatctgatggaaaacttttttattcgatacagCTAATGTGTTTCATCGTGATTTGAAGCCTAAAAATATTCTAGCCAACTCTGATTGCAAGTTGAAGATTTGCGACTTTGGGCTTGCTCGAGTGTCCTTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA