Sequence
atgc intronic sequence ATGC exonic sequencegcaagctttttaatttatatcttcttacaaagttcaagatcgtttttttcattactcttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51820.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 6
gcaagctttttaatttatatc--ttcttacaaagttcaagatcgttttt---ttcattactc-ttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG
| | | ||| | || | || | || |||| ||| ||||| || | | || ||| | | ||||| |||| ||||| || ||||| |||||||||||||||||||| ||||| || || |||| ||||||||||||
gtatgttttacaccttttttcattcattgtgtgcttcactatcttttttaattttctaattcattgcagttttcaattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 6
---------gcaagctttttaatttatatcttcttacaaagttcaagatcgt---ttttttcattactcttgt-tgataattat-tctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG
| | | | ||| ||| | | | | || | | || |||||| ||| | |||| || | ||| | | |||| ||||| || || || |||||||||||||||||||| |||||||| || ||||||||||||| |||
gtatgctttggatcttctataaattaattatgtggatgactatccactttgtccattttttttttatttttgtatggtttctatattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 6
------------------------gcaagctttttaatttatatct-tcttacaaagtt-caagatcgtttttttcattactcttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG
|| |||| | |||| | | || || | || || || | | || ||| || ||| | |||||||||||| ||||| |||||||||||||||||||||||||| |||||||||||||| |||||||| |||
gcatgccagttagagtttttctcctggagtattttgacatatagggataacataacctttccagctcacttgctcctttcttctgatttcctcaaattttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 6
------------------------gcaagctttttaatttatatct-tcttacaaagtt-caagatcgtttttttcattactcttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG
|| |||| |||| | | || || | || || || || || ||| || | ||| | |||||||||||| ||||| |||||||||||||||||||||||||| |||||||||||||| |||||||| |||
gcatgccagttaaactttttctcctggagtattttggcatatagggatagcataacctttccagctcacttgcttttttcttctgatttcccaa-attttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 6
------------------------gcaagcttttta-atttatatcttcttacaaagttcaagatcgt--------ttttttcattactc--ttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG
| |||||| | || | | | | || | || || | || ||| || || | || || || | | ||||| |||||||| || || |||||||||||||||||||||||||| ||||||||||| ||||| ||||||
gcaaagcatattcctctccttgttcctagctttctgcatctggcaccttattttaaatccatactcatctgccttgttcttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ32824 (Selaginella moellendorffii), 3'ss of exon 5
gcaagctttttaatttatatcttcttacaaag-ttcaagatcgtttttttcattactcttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG
|| | ||| || || || | | ||| ||| | | | | |||||||||||||||||||| ||||| || ||||| || ||||| || || | | ||||||||||| |||
--------------------------gtaaggcttctagtatgtgcttgaagtgattct----gattttcagtgtttcagGCAAATGGAGGATTCATCATGAGCGCGAGCCACAACCCTGGCGGTCCCAAGAACGACTGGGGTATTAAG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ34621 (Selaginella moellendorffii), 3'ss of exon 5
gcaagctttttaatttatatcttcttacaaag-ttcaagatcgtttttttcattactcttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG
|| | ||| || || || | | ||| ||| | | | | |||||||||||||||||||| ||||| || ||||| || ||||| || || | | ||||||||||| |||
--------------------------gtaaggcttctagtatgtgcttgaagtgattct----gattttcagtatttcagGCAAATGGAGGATTCATCATGAGCGCGAGCCACAACCCTGGCGGTCCCAAGAACGACTGGGGTATTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacaaagttcaagatcgtttttttcattactcttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG
ttattctc CT-rich tract
ttgttgataattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagctttttaatttatatcttcttacaaagttcaagatcgtttttttcattactcttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA