Sequence
atgc intronic sequence ATGC exonic sequencegtgaagagacaatagatttgatatagccttgttgttagcttgcatatgcttgtcagttaactagtactttatctaaattaatggaatttttggtccaattatgtcagATTGTGGCTGAGTTACCTACTGGTCAAAACTGGAATTTTGATGTTCATTGGTATCCAAAGATGCCTGGAGTTATATCAGCATCTTCAGTTGATGGGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G18830.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G18830.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G36050.2 (Glycine max), 3'ss of exon 8
----------------------gtgaagagacaatagatttgatatagccttg--ttgttagcttgcatatgcttgtcagttaactagtactttatctaaat--taatggaatttttggtccaattatgt--------cagATTGTGGCTGAGTTACCTACTGGTCAAAACTGGAATTTTGATGTTCATTGGTATCCAAAGATGCCTGGAGTTATATCAGCATCTTCAGTTGATGGGAAAA
| | | | |||||| | | || | | |||||| | | | | | |||||| || || | | | |||| ||| | | | ||||||| || || || |||| || |||||||||||||| ||||||||||| | ||| |||||||| |||||||||||||| ||||||| ||||
gtggtgcttttgcctttttttacccatctcatattctgtttgatgagttccagaactgctcgattgcattgacat-ttacaaatatagtacattggctcagtggtgatggtttttcctttttgggtgggggtggggtacagATTGCCTACGAATTGCCAGCTGGGACCAATTGGAATTTTGATGTGCATTGGTATCCCAGGATACCTGGAGTAATATCAGCATCTTCCTTTGATGGAAAAA
upper sequence: AT1G18830.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G01290.1 (Glycine max), 3'ss of exon 8
---------------------gtgaagagacaatagatttgatatagccttgt--tgttagcttgcatatgcttgtcagttaactagtactttatctaaat--taatggaatttttggtccaattatgt--------cagATTGTGGCTGAGTTACCTACTGGTCAAAACTGGAATTTTGATGTTCATTGGTATCCAAAGATGCCTGGAGTTATATCAGCATCTTCAGTTGATGGGAAAA
| | | | |||||| | || || | | |||||| | | | || | ||||||||| || | | | |||| ||| | | | ||||||| ||| || || |||| || |||||||||||||| ||||||||||| | ||| |||||||| |||||||||||||| ||||||| ||||
gtggtgttttgccttgttttacccatctcatattctgtttgatgagttccagtactgcttgattgcattgacctttacattta-tagtactttggctcagtgatgatggtttttcctttttgggtgggggtggggtacagATTGCCTATGAATTGCCAGCTGGGACCAATTGGAATTTTGATGTGCATTGGTATCCCAGGATACCTGGAGTAATATCAGCATCTTCCTTTGATGGAAAAA
upper sequence: AT1G18830.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv13s0158g00140.t01 (Vitis vinifera), 3'ss of exon 8
----gtgaagagacaata--------------gatt-tgatatagccttgttgttagc-ttgcatatgcttgtcag-ttaactagtactttat----ctaaattaatggaatt-tttggtccaattatgt--cagATTGTGGCTGAGTTACCTACTGGTCAAAACTGGAATTTTGATGTTCATTGGTATCCAAAGATGCCTGGAGTTATATCAGCATCTTCAGTTGATGGGAAAA
||||| | |||| |||| | | || |||| | | | || | ||| | || ||| | | ||| | ||| | |||| | | ||| | ||||| | | |||||||| ||| || || ||||| ||||||||||||||| | || ||||| || ||||| |||||||| |||||||| |||||| ||||||| ||||
gtaggtgaaatgccaatttcagccttctttccgattgttgtgtatttctgttttgaacatttcctattttgagcaaattattttggcttttgttctgctatgatgatggtactatttctttcaattcttttgcagATTGTCTGTGAATTGCCAGCTGGTACCAACTGGAATTTTGATATACACTGGTACCCCAAGATACCTGGAGTCATATCAGCGTCTTCATTTGATGGCAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagttaactagtactttatctaaattaatggaatttttggtccaattatgtcagATTGTGGCTGAGTTACCTACTGGTCAAAACTGGAATTTTGATGTTCATTGGTATCCAAAGATGCCTGGAGTTATATCAGCATCTTCAGTTGATGGGAAAA
aattaat putative branch site (score: 3)
tactttatctaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaagagacaatagatttgatatagccttgttgttagcttgcatatgcttgtcagttaactagtactttatctaaattaatggaatttttggtccaattatgtcagATTGTGGCTGAGTTACCTACTGGTCAAAACTGGAATTTTGATGTTCATTGGTATCCAAAGATGCCTGGAGTTATATCAGCATCTTCAGTTGATGGGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG