Sequence
atgc intronic sequence ATGC exonic sequence...gcctcatcaaaatgcctcattcgttttttaccttgtctctgtgcattaggtatcctttagagagtgatgtatcttttctttctctcttcgatcttgctagGTGACTGGTTGGGTGGTAGAGTACCAAGAAAACTTGATTGCACTTGGTGTTGATGATTCACTAGCTCAAGTGTGTTCTGAGAGCGGTTCAATGGATCCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71820.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 8
--gcctcatca-aaatgcc-tcattcgttttttaccttgtctctgtgcattaggtatcct---ttagagagtgatg------tatcttttctttctctcttcg--------------------atcttgctagGTGACTGGTTGGGTGGTAGAGTACCAAGAAAACTTGATTGCACTTGGTGTTGATGATTCACTAGCTCAAGTGTGTTCTGAGAGCGGTTCAATGGATCCTC
||| ||| |||| | | ||| || | || || | ||| | | | || |||| ||| ||| |||| |||| | | ||| ||||||||||||||||| || | || |||||||||||||||| |||||||| ||||| ||||| || ||||| |||||||| || ||| || ||||||| |
gtaccttatctcaaatatcataattttattctcactgcaccttttcagattgtgctccttcggttcaggagtaatgagtaaatattttttacttctgttcttagcaagctcattaatagactaatcactgtagGTGACTGGTTGGGTCGTGCAATATCAAGAAAACTTGATTGGTCTTGGTGTGGATGAATCACTTGCCCAAGTTTGTTCTGAAAGTGGTGCATTGGATCCCC
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 14
gcctcatcaaaatgcctcattcgttttttaccttgtctctgtgc-attaggtatcctttag-agagtgatgtatcttttctttctctcttcgatcttgctagGTGACTGGTTGGGTGGTAGAGTACCAAGAAAACTTGATTGCACTTGGTGTTGATGATTCACTAGCTCAAGTGTGTTCTGAGAGCGGTTCAATGGATCCTC
|||||| | || | | | || || | | | | | | | | | | | | | | || |||| | ||| | || || || |||| ||||| |||||||| || |||||||| || |||||| ||||| || ||||| || ||||| ||||||||||||||||| ||| ||||||||||||
-agtcatcattgtttttcttgttctctatattttctttttctcccgctgaatgttttatgggaaaattatacatctatgcttatgtttttttatgaagc-agGTAACTGGATGGGTGGTTGAATACCAAGATAATCTGATTGGGCTTGGAGTCGATGAGTCTCTAGCCCAAGTGTGTTCTGAGAGTGGTGCAATGGATCCTC
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 13
gcctcatcaaaatgcctcattcgtttttta-ccttgtctctgtgcattaggtatcctttag-agagtgatgtatcttttctt-tctctcttcgatcttgctagGTGACTGGTTGGGTGGTAGAGTACCAAGAAAACTTGATTGCACTTGGTGTTGATGATTCACTAGCTCAAGTGTGTTCTGAGAGCGGTTCAATGGATCCTC
| |||| | | | || | ||| |||||| | | | || | | |||| | | || | | ||| | | | | || | |||||| ||||||||||| || || |||||||| || | |||| ||||||||||||||||| |||||||||||||||||||||| ||| | ||||||||||
---ttatcatagaacttttatcactgtttgtccttgtttttttagtttttttcccttttatcatcataattttttgtttataatttttgtttcttgcaactagGTAACTGGTTGGGTTGTTGAATACCAAGACAATCTAATTGGGCTTGGTGTTGATGATTCTTTAGCTCAAGTGTGTTCTGAGAGTGGTGCTATGGATCCTC
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 13
gcctcatcaaaatgcctcattcgttttttac-cttgtctctgtgcattaggtatcctttagagagtgatgtatcttttctt-tctctcttcgatcttgctagGTGACTGGTTGGGTGGTAGAGTACCAAGAAAACTTGATTGCACTTGGTGTTGATGATTCACTAGCTCAAGTGTGTTCTGAGAGCGGTTCAATGGATCCTC
|| |||| | | | || | ||| ||||| | | || || || | | || | | ||| | | | | || | |||||| ||||||||||| || || |||||||| || | |||| ||||||||||||||||| |||||||||| ||||||||||| ||| | ||||||||||
--cttatcacagaacttttatcactgtttgttcttgttttttagcttttttcccttttatcatcataattttttgtttataatttgtgtttcttgcaactagGTAACTGGTTGGGTTGTTGAATACCAAGATAATCTAATTGGGCTTGGTGTTGATGATTCTTTAGCTCAAGTTTGTTCTGAGAGTGGTGCTATGGATCCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaggtatcctttagagagtgatgtatcttttctttctctcttcgatcttgctagGTGACTGGTTGGGTGGTAGAGTACCAAGAAAACTTGATTGCACTTGGTGTTGATGATTCACTAGCTCAAGTGTGTTCTGAGAGCGGTTCAATGGATCCTC
tatcttttctttctct CT-rich tract
tatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcctcatcaaaatgcctcattcgttttttaccttgtctctgtgcattaggtatcctttagagagtgatgtatcttttctttctctcttcgatcttgctagGTGACTGGTTGGGTGGTAGAGTACCAAGAAAACTTGATTGCACTTGGTGTTGATGATTCACTAGCTCAAGTGTGTTCTGAGAGCGGTTCAATGGATCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA