Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtgacttcccaaagattgtgatcttcttttcttttaactgttctgatggatgacattgaatttgatctcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46860.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 3
------------gtaatgtgacttccca---aagattgtgatcttcttttcttttaactgttctgatggatgacattgaatttgatctcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
| ||| | || | | | || | | | ||| | | || | | | | ||| |||||||| ||| |||||||||| || || ||||| || ||||| ||||| |||||||| || || | || |||||||||||||| | ||||| || || |
gtctgtaatcaaacactgtatttatacactcacgtcagggaccatatgctctgtggaacttttttaccatttgggctcttgttg--tacagGTTGATCGGGTCTTGTACTCGTCAGTGGTTTACCCCCACAACTACGGCTTCATCCCTCGAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGC
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G015418_T01 (Zea mays), 3'ss of exon 4
----------------------------------------gtaatgtgacttcccaaagattgtgatcttct--tttcttttaactgttctgatgg-atgacattgaatttgatctcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
| | | || || || || | || | | || | |||| ||||| | | | || |||||||| || | | ||||| || || || || |||||||| ||||| ||||| ||||| ||||||||||||||| ||||| | ||||| || ||
gtaaagacgattatctgttaacatttaaggtcacgggaaagatacaaaaaaaaaaaagagttaccattttttatttattcctgacggcactgaaaatgtgacaattatgcttccct-agGTTGACAGGGTGCTATACTCATCAGTGGTCTACCCACACAACTACGGTTTCATTCCACGAACATTGTGTGAAGACGGAGATCCAATGGATGTGCTGGTGT
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
-----------------gtaatgtgacttcccaa----agattgtgatcttcttttctt-ttaactgttctgatgga-tgacattgaatttgatc-tcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
| || |||| ||| ||||| | || || | | || | | | || || | || || ||||||||| ||| | |||||||| || ||||||||||| || || || || ||||||||| | || ||||||||||||| ||||| |||||||| | || |
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 3
----------------------------------------gtaatgtgacttcccaaagatt------gtgatcttcttttctt--ttaactgttctgatg--gatgacattgaatttgatctcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
| ||| ||| | ||||| |||| || || | | || | | ||| | || | | | || |||||||| ||| | ||||| || || |||||||||||||| || || || || ||||| || ||| ||||||||||||| ||||| ||||||| | || |
gtacaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcctatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G16860.1 (Glycine max), 3'ss of exon 1
----------------------------------------gtaatgtgacttcccaaagatt------gtgatcttcttttct-tttaactgttctgatgg--atgacattgaatttgatctcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
| ||| ||| | ||||| |||| || | | || | | ||| | || || | | || |||||||| ||| | ||||| || || |||||||||||||| || || | || ||||| || ||| ||||||||||||||||||| ||||| | | || |
gtacaaaccaattgcctggttactggaatgaaagcccctactgctgtagcttgaaatagatttcccagatgatttttccccatacccatctatctttatgcttacgattttcgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGATTTTATCCCTCGCACACTGTGTGAAGACAACGATCCAATTGATATTTTGGTTC
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
----gtaat-----gtgact--tcccaaagattgtgatcttcttttctttt--aactgttctgatggatga---------cattgaatttgatctca-------gGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
|| || |||||| | ||| | | ||||| | |||| | ||||| ||| | | | || | || | |||| |||||| || ||||||||||| || ||||| |||||||||||||| || ||||| ||||| || | ||||| || | ||||| ||||||| || |||
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCAMapped 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|19878118|gb|AU238949.1|AU238949EST: AGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG GTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTC
genomic: AGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAGgtaatgtgac ... ttgatctcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTC
EST:
gi|86073611|gb|DR369368.1|DR369368EST: AGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG GTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTC
genomic: AGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAGgtaatgtgac ... ttgatctcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgatcttcttttcttttaactgttctgatggatgacattgaatttgatctcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
ttcttttcttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtgacttcccaaagattgtgatcttcttttcttttaactgttctgatggatgacattgaatttgatctcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA