Sequence
atgc intronic sequence ATGC exonic sequence...tcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G50500.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 3
tcttatcgttcatgctcttta--cctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttctt-ttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
|| | | | | |||| | | | | || | | | ||| |||| |||| ||||| ||| || | ||| | || | || |||||| |||||||||||||| |||||||| || |||||||| ||||| |||||||| || || ||| |||| || ||||||||||||| |||
-ctgtgcatgtgtcttgtttagcctttcggggaatttgtgcctggaatcttttttaacttta--ttctgatcatgtcatgacttttttttcttcatttgtcagTCGTCTGTTCTTCATTCGCAACCAAAATCTACTGTTGGAACTCCGGCATACATCGCTCCTGAGGTTCTGCTGAAGAAGGAATATGATGGAAAG
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 5
tcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtatta----actatgcgtttcttttctt-cagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
| | | | | | | | | | || | | || ||| | ||||| |||| || || ||| | ||||| | || ||||| || ||||||||||| |||||||| ||||| ||||| ||||| || || ||||| ||||| || | || | ||||| ||||| |||
----actttctgtagtagtgaaa-agaagagagaactttcgctagatttttctcgatgtgattgctgcctggataatattgtactgttgctttctgattttgcagTCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAG
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
-tcttatcgttcatgctctt-tacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctca-agtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
|||| ||| | | | || ||| | | | | ||| || ||| ||| || | | || | || | || || ||| ||||| |||||||||||||||||||| |||||||||||||| || ||||| || |||||||| || |||| | | | |||||||||||||||
ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagg--gttgtcagtttccttttaactaacaataccatgcattc-ttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
-tcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctca-agtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
|||| ||| | | | || | | | || | ||| || ||| ||| || | | || | || || || ||| ||||| ||||||||||||||||| || ||||| |||||||| || ||||| || |||||||| || || | | | | |||||||||||||||
ggcttaatgtttacacgatggtagtaga-ataatgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcattt-ttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
tcttatcgttcatgct-ctttacctacatgtgtttcctactaa-gtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
| | | | | | | || || ||| || | || | ||||| | ||| ||| | ||| | | ||| || | || |||||||| || |||||||| ||||||||||||||||| || ||||||||||| ||||| ||||| | | | ||| || ||||||||||||
-atagtggattttacaacaatagatagatgaattgtttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatg-gtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
tcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttga-----tttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
|| | | | | | ||| | || | | | ||| |||||| | ||||| ||| | | ||| | | | ||| || | ||| |||||||| || |||||||| ||||||||||||||||| || ||||||||||| ||||| ||||| | | || ||| || ||||||||||||
---tacaatagtggatttacaactatagatgatcattgtttcctgt-tgtttttgttttgagtttttttttccccaaatctgattgatg-gtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 5
tcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgc-tcaagtattaactatgcgtttcttttctt-cagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
|| || ||| | || | || | | ||| | | || | ||| | | ||||||| || | | || ||| || | |||||||| || |||||||| ||||| ||||||||||| || ||||| ||||| ||||| ||||| | | || || || ||||||||||||
-tttttctttcgtcctttgtattctattttattttaaagaatttgaattgttttgatc-aatttctgtatcctgcaaatgtaatagattttgttattggcagTCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
tcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctt---tgatttctg---ctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
| | | | | |||| || | | | | ||| || || ||| || | | || | || ||| || | |||||||| || |||||||| ||||| ||||||||||| || ||||| ||||| ||||| ||||| | | || || || ||||||||||||
-----aaatagaggtcatccatgtacaagtaatgacacatcaaggtccattaatagttgatcaattactatatcctacaaatctaatagat-tttgttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
tcttatcgttcatgc-tctttaccta-catgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtatt--aactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
| | | | | || | | || || | | ||| || | | | | | | | | | || | | | ||||||||| || |||||||| |||||||| ||||||||||| ||||||||||||||||| ||||| | | | | || ||||| |||||||||
----agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaaatctgacagtggcacttctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAGMapped 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|164018896|gb|ES076427.1|ES076427EST: CTCGTTTAAAAATATGTGATTTTGGATATTCCAAG TCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATAC
genomic: CTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGgtactattta ... ttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATAC
EST:
gi|116422506|gb|EG465098.1|EG465098EST: ATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAG TCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATAC
genomic: ATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGgtactattta ... ttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
tattaac putative branch site (score: 1)
tgcgtttcttttcttc putative PPT
tattaactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
- - - - - -atgctct
- - - - - - - - - - acctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctca