Sequence
atgc intronic sequence ATGC exonic sequenceGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtgatctcaagcattgtgatcatatatacttgtaacatgggtgttaatcggtctgatgattcatacctctctcatcattgatgccag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55520.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 5'ss of exon 7
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagt-gatctcaagcattgtgatcatatatacttgtaacatgggtgttaatcggtctgatgattcatacctctctcatcattgatgccag
||||| ||||| ||||||||||| ||||| |||||||| ||||| || || ||||| || || |||||||| |||||| |||||||||||||||||||| || | |||| | | | | | |||| || | | | ||| ||| | ||| | | |
GATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGTgtaagttgagtccttgcatgcctttttaggacgcctttcacatttgttatg-ttgttcttatgtcctgtgccttttgtgttaacag------
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 5'ss of exon 6
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagt-gatctcaagcattgtgatcatatatacttgtaacatgggtgtta-atcggtctgatgattcatacctctctcatcattgatgccag
|| || ||||| ||||||||||| || || |||||||| ||||| || || ||||| || || |||||||| |||||| |||||||||||||||||||| || | |||| | | ||| || | || ||||| ||| ||| | | ||| | | |
GACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGTgtaagttgaatccttgcatgtttttttaggatatttctttcacatatgttatgctattctcatgtcttgtgccttttgtcttccag-------
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 5'ss of exon 4
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagt-gatctcaagcattgtgatcatatatacttgtaacatgggtgtt-aatcggtctgatgattcatacctctctcatcattgatgccag------------------------------------------------------------------
||||| ||||| ||||||||||| || ||||||||||||||||| || ||| | || || || ||||| || |||||| | || ||||| ||||||||| ||| | | || | | | | || || || ||| | | | || || | | || || |||
GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgattacttacttttttacattgt---ctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcag
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G161418_T05 (Zea mays), 5'ss of exon 7
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagt-----gatctcaagcattgtgatcatat--atacttgtaacatgggtgttaatcggtctgatgattcatacctctctcatcattgatgccag
||||||||||| ||||| ||||| ||||| ||||||||||| || || ||||||||||| || |||||||| |||||| |||| |||||||||||| || ||| || | | || | || ||| || | | ||| || | | | | | || | || ||
GATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGTgtatgtccaaggatggtttattttatcaccacagtaattcttttaccctttttgtctgcattcttggataatgacatttttcatttgttttatag---
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgta-----agtgatctcaagcattgtgatcatatatacttgtaacatgggtgttaatcggtctgat--gattcatacctctctcatcattgatgccag
|| |||||||| ||||| ||||| ||||| |||||||| || || || ||||||||||| || ||||| || |||||| |||| |||||||||||| | |||| | ||| |||| | || || | || | | || || || | || | || | | |||| | | |
GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcaca-attttttttacctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag-
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA19G28780.1 (Glycine max), 5'ss of exon 7
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtgatctcaagcattgtgatcatatatactt----gtaacatgggtgttaa--tcggtctgatga-ttcatacctctctcatcattgatgccag-----
||||||||||| ||||||||||| ||||| ||||||||||| ||||||||| | ||||| |||||||| || || ||||||||||||||||||||||||| | || | ||||| | | || || | | || || | | || | | ||| | || | |||| | |
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGTgtaagtg---tgaaatgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcagtcctatatatggtc
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtgatctcaagcattgtgatcatatatactt----gtaacatgggtgttaa--tcggtctgatga-ttcatacctctctcatcattgatgccag-----
||||||||||| ||||||||||| ||||| ||||||||||| ||||||||| | ||||| |||||||| || || ||| ||||||||||||||||||||| | ||| | ||||| | | || || | | || || | | || | | ||| | || | |||| | | |
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtg---tgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcagtcctacatatggtc
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA16G25450.3 (Glycine max), 5'ss of exon 7
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagt---gatctc------aagcattgtgatcatatatacttgtaacatgggtgttaatcggtctgatgattcatacctctctcatcattgatgccag--
||||| || || ||||||||||| ||||| ||||||||||| |||||||| |||| || ||||||||||| || ||| |||||||||||||||||||| || | || | || || | | | | || | | | | | | | || || | || ||| |||||
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttttaattttttgggaaaataaattggtccctggtgacttttatatcagaatattttgttttcacaatcaatgtttggct-atc-ctgatgtttagg
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtgatctcaagcattgtgatcata---tatacttgtaacatgggtgttaatcggtctgatgattcatacct-----ctctcatcattgatgccag--
||||| || || ||||||||||| ||||| ||||||||||| |||||||| |||| || ||||||||||| || ||| |||||||||||||||||||| | | | ||| || ||| ||| | ||| | | | | | | | || | || ||| || ||| |
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttagtt-attttttgggaaaataattcatagggttggattggttactggtgatttttacattaaatttttttttgctttcacaatcaatgtttggc
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA18G44460.1 (Glycine max), 5'ss of exon 6
-GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtgatctcaagcattgtgatcatatatacttgt-----aacatgggtgttaatcggtctgatgattcatacctctctcatcattgatgccag------
||||||||||| ||||| ||||| ||||| |||||||| || ||||||||| | || || |||||||| || || ||| ||||||||||||||||||||| | || || | ||| | | | ||| || | | || ||||| |||| | | | |||| | |
GGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGtgtaagtg---tgaaatgttataatcttctgttcttcctggtgaatttcttggaaaaatggtctacaaattcctgtcctagttatcagtactatatatggtcc
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA02G06370.1 (Glycine max), 5'ss of exon 3
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtg---atctcaagcattgtgatcatatatacttgtaacatgggtgttaatcggtctgatga--ttcatacctctctcatcattgatgccag--------
||||| || || |||| |||||| ||||| ||||||||||| |||||||| | ||| || ||||||||||| || ||| |||||||||||||||||||| || | || || | ||| | | || || || || || ||| ||| || ||| | | | ||| | ||
GATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCAT-ATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagtttttattttttattttttgggaaaata-attcataggattgg-attggtc--cctggtgacttttatatcaaaatattttttgttttcacaatcgatg
upper sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 5'ss of exon 7
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtgatctcaa-------gcattgtgatcatatatac---ttgtaacatgggtgttaatcg-gtctgatgattcatacctctctcatcattgatgccag
||||||||||| |||||||| || ||||| |||||||| ||||||||||| ||||||||||| |||||||| |||||| |||| || || || ||||||||| || | | | || || ||| || | ||| || | || | |||| | | ||| |
GATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGCgtaagtgatgacattgttttcggagttcaattatttatttatttttctgtaaaaatgtgaaccatacttgggaagtcatgtttaaactaaggttggaaca--Mapped 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|47831853|gb|CK121537.1|CK121537EST: TCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT TACGAGCCTGAGCTATTTCCAGGATTGATATATAGGATGAAACTTCCAAAG
genomic: TCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtgatc ... ttgatgccagTACGAGCCTGAGCTATTTCCAGGATTGATATATAGGATGAAACTTCCAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgtaagtgatctcaagcattgtgatcatatatacttgtaacatgggtgttaatcggtctgatgattcatacctctctcatcattgatgccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG