Sequence
atgc intronic sequence ATGC exonic sequencegtacttgttgattaggagtagtgtatcttgtgattacttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53170.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
gtacttgttgattaggagtagtgt-atcttgtgatta-cttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
||| | ||| | ||| | | | |||| | || | | || |||||||| | || ||||||||||||| || |||||||| ||||||||||| ||||| ||||||||||| || |||||||| |||||||| ||||| |||
-----------------gtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctatt--gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10
gtacttgttgattaggagtagtgtatcttgtgattacttccgctagtttgc--aggaatataatagtactttgctttctatt-----ttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
| |||| |||| |||||| | | | | | | || | | || | |||||| | ||| || | ||||||||||| || |||||||||||||||||||| || || |||||||| || || |||||||| |||||||||||||| |||
-----------gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 10
gtacttgttgattaggagtagtgtatcttgtgattacttccgctagtttg--caggaatataatagtactttgctttctatt-----ttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
|| | |||| |||| | || | | | | | ||| | | || | |||||| | ||| || | | ||||||||||| || |||||||||||||||||| | || || |||||||| || || |||||||| |||||||||||||| |||
-----------gtatgc-tagtctatcacattatcaaatagagcaatatattcagaactttacctgactcttgcttccaattgatcttttatcttacagGGAATAATTGTGATGGCTGCAACAAACTTGGCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 10
gtacttgttgattaggagtagtgtat-cttgtgattacttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
|| ||| ||| | | |||||| | || |||||| | | || | || | || || | || ||||||||||||| || |||||||||||| |||||||||| |||||||| ||| | ||||| || ||||||||||||||||||
------gtatatttcaagttttaaacatttgtgagtgttta-attagtttctctctgtttcctaat---ttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 10
gtacttgttgattaggagtagtgtatcttgtgattacttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
| | || || | || ||| |||| || |||| || ||| | | | || ||| | || | ||||||||||| | |||||||||||||||||||||||||| ||||| |||||| | || || || || ||||||||| | |||
-------gtatctttgaacagcttggagtgcaatttgttcctctggttt-tagaaat----tgattcattattttatcttct--------agGGAATAATATTAATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACGAGGCCTGGCAGATTTGATCGGCAT
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 2
gtacttgttgattaggagtagtgtatcttgtgattacttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
| | || ||| | || ||| |||| || |||| ||| | || | |||||| | || ||||||||||| | |||||||||||||||||||||||||| ||||| |||||| | || || || || ||||||||| | |||
-------gtatctttgaacagtttggagtgcaattcgttcctctggttt------------tagaaattgattcattattttatct-tgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 10
gtacttgttgattaggagtagtgtatcttgtgattacttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
| | | | | |||||| ||| | | ||| | || | | || ||| | |||||| | || |||| |||||| | ||||| |||||||||||||||||||| |||||||||||| | |||||||| ||||||||||| || |||
----------gtaacatatggacaaacttgtg-ttattagtgaatatttttctgcattt--ttttaacttggataatatttt--tcttgtagGGCATAATATTGATGGCAGCAACAAACTTGCCTGATATTCTTGATCCAGCTTTAACAAGACCTGGTAGATTTGACAGGCAT
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S9_238V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------------------gtacttgttgattaggagtagt-gtatcttgtgattacttccgctagtttgcaggaatataa-tagtactttgctttctattttg----gttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
||| || ||| || || | | | || | | | |||| | | | ||| | | || || ||| || ||||||| || || || | || || ||||| | || || | ||||| |||||||||||| |||| ||||||||||||||||||
gttagttcacttcaatttgattggttactgaacatgttgcctttggttgatatcaaaccgatgtagagtagaagcggtcatgtatatacatcatgatcttttgtttatttatttcttgcttgtattgtatgtttgatattgttatattctgcagGGCATCATTGTGCTAGCAGCTACAAATCTCCCCGAGACTCTTGACCCAGCTCTGACACGACCTGGTAGATTTGATAGACATMapped 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|125064739|gb|EL132257.1|EL132257EST: AGACATTGCATCAACTACTTGTTGAAATGGATGGTTTTGAGCAGAATGAG GGAATAATAGTTATGGCTGCAACAAA
genomic: AGACATTGCATCAACTACTTGTTGAAATGGATGGTTTTGAGCAGAATGAGgtacttgttg ... ggttatgcagGGAATAATAGTTATGGCTGCAACAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
aatataatagtacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgttgattaggagtagtgtatcttgtgattacttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC