Sequence
atgc intronic sequence ATGC exonic sequencegtctaccttctctattctccactcttatccatgactctttgttgtaagcttttacgctgatattatcttgtttcctttctaaatcattaagACTCATATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G61850.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G61850.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os07g33670.1 (Oryza sativa), 3'ss of exon 11
------------------------------------gtctaccttctctattctccactcttatccatgactc----tttgttgtaagcttttacgctgatattatcttgtttcctttctaaatcattaagACTCATATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG
|| | | || | | | | | | ||| |||||| | | || ||| || ||| ||| || |||| | |||| ||||| ||||| || || || || |||||||| ||||||||||| || ||||| ||||||||| | |||||||| || | ||| |||||
gtagatattcctaaacttagttgtggatattgttttgtgcaagaacagtaggcctctatttgtttgagtcctcaagatttgttatccaccgcagttcttatagccctttttttttcttcctttctcttcagACGTAAATCGTTGGCAGGATGGAGCTATTGTAGCCAACAATCCCACAATCTTTGCGATAAGAGAGGCACAACTTTTGTGGCCTGATACGAGAATAGATTG
upper sequence: AT1G61850.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G426556_T01 (Zea mays), 3'ss of exon 9
--------------------------gtctaccttctctattct---------ccactcttatccatgactctttgttgtaagcttttacgctgatattatcttgtttcctttctaaatcattaagACTCATATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG
|||| || | || | | | || | | | | ||| | | | | | | | | |||| || | | ||| | | | ||| || |||| ||||||||||| || || || || ||||||||||||||||||||||| ||||||||||||||| | ||||| || || ||| |||||
gtaatatttgtaagctcagttatggcatctattttgtgtagtacagaatatgccttgttttcttgaaggcctcttgatatcaaatgctccttggttgttatgttttcttcttatcattttttccagATGCAAATCGTTGGCAAGATGGAGCTATTGTAGCCAACAATCCTACAATCTTTGCCATTAGAGAAGCACAACTTTTGTGGCCAGATGCACGAATAGATTG
upper sequence: AT1G61850.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G451672_T01 (Zea mays), 3'ss of exon 5
---------------------------------gtctaccttctctattctccactcttatccatgactctttgttgtaagcttttacgctgatattatctt-gtttcctttctaaatcattaagACTCATATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG
| | | | | | | || | || | | ||| |||| ||| | | || | | | | || || || || | | || ||| | |||| ||||||||||| || || || || ||||||||||| ||||||||||| ||||||||||||||| | ||||| || ||| ||| |||||
gtaatatttgtacactcagctatggtttctattttgtgcaatgtagactgtcttgttttcttgaagaccttttgatgtcggatgttcctcagttgccatttttattattgttaccattttttcagATGCCAATCGTTGGCAAGATGGAGCTATTGTAGCCAACAATCCTACGATCTTTGCCATTAGAGAAGCACAACTTTTGTGGCCAGATACACGAATAGATTG
upper sequence: AT1G61850.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G01850.1 (Glycine max), 3'ss of exon 11
-------------------------gtctaccttctctattctccactcttatccatgactctttgttgtaagcttttacgctgatattatcttgtttcctttctaaatcattaagACTCATATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG
| || || | | | | ||| || | ||| | | |||| | |||| || |||| | |||||| | |||||||||||||||||||||||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||| ||||||||||| ||
gtactgattactgtgctgttgtgtgcatcaatttggctgtattttagttttagttatttccatttctgtattgtttttttacatttatttattttcatcctgcaacgtgccttaagATGTCAACCGCTGGCAAGATGGTGCAATAGTGGCTAACAATCCTACAATTTTTGCCATAAGAGAAGCACAACTTCTGTGGCCTGATACAAAAATTGACTG
upper sequence: AT1G61850.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 10
--------------------gtctaccttctctattctccactcttatccatgactctttgttgtaagcttttacgctgatattatcttgtttcctttctaaatcat----taagACTCATATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG
|| | | | || || | | | | | || | | | || | || | || ||| | | || | ||| ||||| | ||||||||||||||||| |||||||| |||||||||||||| |||||||| ||||||||||||||||| ||||| || ||||||||||| ||
gtactgattactctgctgttgtttgcatcaattaggctgtattttagttttagttatttccatttctgtattgttatttatgtgtatttattttcatcctgcaacatgccttaagATGTCAACCGCTGGCAAGATGGTGCGATAGTGGCTAACAATCCTACAATTTTTGCCATAAGAGAAGCACAACTTCTGTGGCCAGATACAAAAATTGACTG
upper sequence: AT1G61850.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------gtctaccttctctattctccact------cttatccatgactctttgttg----taagcttttacgctgatattatcttgtttcctttctaaatcattaagACTCAT---------ATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG
| | | || || | | ||| | | | || || ||| |||| ||| || || | || |||| ||| | | ||| | |||| ||||||||||||||||||||||||| || || |||||||| | ||| |||| || ||||||||||| ||||||||||||||| ||||||
gtactgtctttctgtgcttgcttgaaatgactcatcacttggcatttgcttttctggttttatgttgaatgccttgtgctttacctctttttggttctaagagtttgttttgtgtttcttttttttctttttttcctaattcaatttcatcagACATGAATCGCTGGCAAGATGGTGCAATAGTAGCTAATAATCCTACTGTTTTTTCCATGAGGGAAGCACAACTCTTATGGCCTGACACAAGAATTGACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgttgtaagcttttacgctgatattatcttgtttcctttctaaatcattaagACTCATATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG
ttctaaa putative branch site (score: 2)
tttctaaatcattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctaccttctctattctccactcttatccatgactctttgttgtaagcttttacgctgatattatcttgtttcctttctaaatcattaagACTCATATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC