Sequence
atgc intronic sequence ATGC exonic sequenceATGAGACATTCCGGTTCTTGGCACGTATATATAGCAAATCTCACCGTAATATGTCTTTGAGCAAAGAATTTGAGGAAGGAATCACCAATGGAGCATCCTGgtatcacatcaagtccccttactctgtcttattcaacaaatgagtttcttggttaatgctttaagcaaaacgctctacag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71696.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71696.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os06g05240.1 (Oryza sativa), 5'ss of exon 10
ATGAGACATTCCGGTTCTTGGCACGTATATATAGCAAATCTCACCGTAATATGTCTTTGAGCAAAGAATTTGAGGAAGGAATCACCAATGGAGCATCCTGgtatcacatcaagtccccttactctgtcttattcaacaaatgagtttcttggttaatgctttaagcaaaacgctctacag---------------------------------
|| |||||||||||| | ||||| | ||||| |||| ||| ||| ||||||||||||||||||||| | | ||| || || |||||||||| ||||||| | | | | | | || | ||| | |||| | || ||| || | ||
ATAAGACATTCCGGTACATGGCATCAGTTTATAGTCAATCGCACTATAACATGTCTTTGAGCAAAGAATTTAAAGGAGGGATTACAAATGGAGCATTCTGgtataaaactagttttgtattattgctccttatcattttttttatttcatatcaaacattttgttgctgctacttttcatgctaactagcaatctatgcttttttgtgttgag
upper sequence: AT1G71696.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G106683_T02 (Zea mays), 5'ss of exon 10
ATGAGACATTCCGGTTCTTGGCACGTATATATAGCAAATCTCACCGTAATATGTCTTTGAGCAAAGAATTTGAGGAAGGAATCACCAATGGAGCATCCTGgta------tcacatcaagtcc---ccttac------tctgtcttattcaa----caaatgagtttcttggttaatg-ctttaagcaaaacg-ctctacag------------
|| ||||||||| | | ||||| | | ||||| |||||| ||| ||||||||||||||||||||||| | ||| || || |||||||||| |||||| | | ||||| | | | | | | |||| | | | ||| | | || |||| | |||| | | |
ATAAGACATTCCAGCACATGGCATCTGTGTATAGTCGGTCTCACTATAACATGTCTTTGAGCAAAGAATTTGAAGGAGGGATAACAAATGGAGCATTCTGgtaaacgaacaatagcaagttcatacttcatatgagatttcctttatctaggtactaggtaggttgtgtatgtgttggctttgaatcaaacaacatcattgcttgtggtccag
upper sequence: AT1G71696.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G127941_T01 (Zea mays), 5'ss of exon 8
ATGAGACATTCCGGTTCTTGGCACGTATATATAGCAAATCTCACCGTAATATGTCTTTGAGCAAAGAATTTGAGGAAGGAATCACCAATGGAGCATCCTGgtat-cacatcaagtccccttactctgtcttattcaacaaatgagtttcttggttaatgctttaagcaaaacgctctacag
|| ||||||||| | | ||||| | | ||||| |||||| ||| ||||||||||||||||||||||| | ||| || || |||||||||| |||||| || | | | || | | || || | | | || || ||| | |
ATAAGACATTCCAGCACATGGCATCTGTGTATAGTCGGTCTCACTATAACATGTCTTTGAGCAAAGAATTTGAAGGAGGGATAACAAATGGAGCATTCTGgtaaacagacaatagcaagttcatatttcataattcatatgagatttcctttatctag-----------------------
upper sequence: AT1G71696.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv18s0157g00050.t01 (Vitis vinifera), 5'ss of exon 10
ATGAGACATTCCGGTTCTTGGCACGTATATATAGCAAATCTCACCGTAATATGTCTTTGAGCAAAGAATTTGAGGAAGGAATCACCAATGGAGCATCCTGgtatcaca--------tcaagtccccttactctgtcttattca---acaaatgagtttcttggt----taatgctt-taagcaaaacg-ctctacag---
|||||||||||| ||| ||||| | ||||||| ||||| | || |||||||||||||| |||||||| | |||||| || |||||||||| |||||| | | | | | | | | | | | | ||| |||| | | || || | | || ||||| | ||||||
ATGAGACATTCCAGTTTATGGCAAGCGTATATAGTCGTTCTCATCACAACATGTCTTTGAGCAAGGAATTTGAAGGAGGAATTACAAATGGAGCATTTTGgtatgaaaatttagaattcaattctcatgatgttcatcaatcatgaacaagaaattgcattagtacgacagtttttctaagcttcctgattctacacttgMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|124777828|gb|EH867771.1|EH867771EST: GGAGCATCCTG GTACCCAATTTATGGTGGCATGCAAGACTGGAATTACATATATGGGG-ATG
genomic: GGAGCATCCTGgtatcacatc ... cgctctacagGTACCCAATTTATGGTGGCATGCAAGACTGGAATTACATATATGGGGGATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGAGACATTCCGGTTCTTGGCACGTATATATAGCAAATCTCACCGTAATATGTCTTTGAGCAAAGAATTTGAGGAAGGAATCACCAATGGAGCATCCTGgtatcacatcaagtccccttactctgtcttattcaacaaatgagtttcttggttaatgctttaagcaaaacgctctacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA