Sequence
atgc intronic sequence ATGC exonic sequencegtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcattagtccttggttaaatatacttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G12000.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
gtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcattagtccttggttaaatatacttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
| | | | || | | || || | || | | || | ||||| || || || | ||| || | | || ||||| | ||| | | | | ||||||| ||||| |||||||||||||| || ||||||||||||||||| || |||
-------------------tgctgatggttaggt----cgctgcatgaaatataca-cacttttcctt--tttaaggggctctcttatttcag---gtacgattttaattttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 3
gtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcattagtccttggttaaatatac-ttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
|| || |||| | | || || || | || || | | || || | | || | |||| ||| |||| | | | || | ||||||| ||||| ||||||||||||||||| ||||||||||||||||| || |||
------------------------aaacttctttaacacacacacacacatatgacatatgtatgtatgtgtacacacacattatttccttttgatgatgca-ttaaaattttgtct-----cttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 1
gtacttggattcagatccttccacaagatttgaatttacac-tccactagatgtggagcattagtccttggttaaatatacttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
| | | ||| | || | || | ||| | || |||| | |||| | || || || | | | ||||| | | ||||| ||||||||||||||||||| |||||||||| |||||||||||||| || || |||
----------------------aaatgttttcagttgaagtatcttgctgttgtttcgattttttcctggaaataataatcatgagattgcaacacctaataggagtaatt--tctgttggt------agGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 3
gtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcattagtccttggttaaatatacttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
| || | | | | | | | || |||| | || | ||| | | || | | || | | | | ||| || | |||||||| ||||||||||| |||||||| || |||||||||||||| || || |||
-------------------------gaaactgtcatcataatttgttgtaagcatagaattactgatttttgtaat-caatgatcacaagattttgacatctattaataaccatttctgct---ggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 3
gtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcatta--gtccttggttaaatatacttg----tctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
| | | | | | | | | ||||| | ||| | || |||| | || || | | || | || | | ||| || | |||||||| ||||||||||| |||||||| || |||||||||||||| || || |||
--------------------------------tctccataatttgttgtaagagaaacattactgattttgttaaattataatcaatgatcattagattttgacatcttttaataaccatttctgct---ggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 3
gtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcattagtccttggttaaatatacttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
| | | ||| |||| | | | | ||| | | | || || | ||| | || || | ||| | | ||| | ||| || ||||||||||||||||||| ||||||| || |||||||||||||| || || |||
----------------------aaatgttttcaattgaggtgtc--ttgctgttg--tttcgattttttcctagaaataataatcattcgattgcgacatc-taataggaataatttctgtt--ggtagGGTGGTTTTGACATGATTCGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 3
gtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcattagtccttggttaaatatacttgtctttttaagtcgatgtggttataattctttttttggtctcaa--cagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
| ||| || | | | | || || | || | | | | | ||||||| | | || | | |||||||||||||| |||||||||||||| ||||||||||||||||| || || |||
-------------------------------gcattcacgcacattttatctatgtgctcatgtatgcacacaggcatgtgataccaccaatatagcctcaacttgtattctttgtcttgttttatatcagGGTGGTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGMapped 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|125221108|gb|EL235193.1|EL235193EST: GCAAATATGTTGAGTTGAATGCTGAATATATTCAGCCTTACAGAAACCAG GGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAAC
genomic: GCAAATATGTTGAGTTGAATGCTGAATATATTCAGCCTTACAGAAACCAGgtacttggat ... gtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAAC
EST:
gi|116438055|gb|EG480647.1|EG480647EST: GCAAATATGTCGAGTTGAATGCTGAATATATTCAGCCTTACAGAAACCAG GGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGAC
genomic: GCAAATATGTTGAGTTGAATGCTGAATATATTCAGCCTTACAGAAACCAGgtacttggat ... gtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatacttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
ttctttttttggtctc CT-rich tract
ttataattcttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcattagtccttggttaaatatacttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA