Sequence
atgc intronic sequence ATGC exonic sequencegtacctattaagttgtaaaggaaaaaaaaccataagttgaataggatgagtctgtgttattgtagtctgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19990.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 6
gtacctattaagttgtaaaggaaaaaaaacca-taagttgaataggatgagtctgtgttattgtagtc-tgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
||| | ||| ||| | | | || | || | |||| | | | | | || || |||| |||||||| ||||||| |||||| | || || || ||||||| || ||||| |||||||| | || || ||||||||||||||||||||||||||||| ||
------------------------gtgtgccactgctttgcatatgttatatgtgccgattaataaccgtgaaggagtttattgtgacacgtta-----aatgttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
gtacctattaagttgtaaaggaaaaaaaaccataagttgaataggatgagtctgtgttattgtagtctgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
| ||| | ||| ||| ||| || | || || || | | ||| || | | || ||| | |||||||||||||||| || || | || || ||| |||||||||| ||||| |||||||| | || || ||||| ||||||||||| |||||||| || ||
-------------------------gtacacatcacttgtgctcctgtgtgctggatta--gtgatttgtaaatgtata-acagttatgatgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 6
gtacctattaagttgtaaaggaaaaaaaaccataagttgaatag-gatgagtctgtgttattgtagtctgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
| | | || | | ||| | | ||||| | ||| | ||||| | |||| | ||| || | | | || ||| | |||||||||||||||| ||||| | || || ||| |||||||||| ||| | |||||||| | || || ||||| ||||| ||||| |||||||| || ||
-------------------gtacacaatcacttgtgttcctttgcgatgaattagtgat-ttgtaat---aaatgtataacaa--tcgtgatgttttaaatatttaatgcagGTTTTGATGGCAACAAACAGAATAGACATTTTGGATCAAGCCCTTTTGAGGCCTGGCCGCATAGACAGGAAGATTGAGTTTCCAAATCCTAACGAGGAC
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 6
----------------------------------------------gtacctat-taagttgtaaaggaaaaaaaaccata--agttgaataggatgagtctgtgttattgtagtctgaaattgctgaca-gagtcat--attctctttaatgact-----------------gttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
| ||| | ||| | ||| ||| | || ||||||| | | | ||| | | |||||| ||| | |||| | ||||| | | | | ||| ||||||||||||| |||||||| |||||||| ||||||||||| || || || |||||| | ||||| |||| ||||||||||| || ||||||||||||
gtaaaggagctatactgttatgtgtattaaggggaattttaaagctagtcttatgtccactgttctgaaaagaaatctgtaacagttgaacttaacagatattatttactct-gtctgactcatttgagatgagttctcaattctttgtggaggttctgaagataaattttcaattgtagGTTTTGATGGCCACAAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCTGGACGGATTGACCGGAAGATTGAATTTCCAAACCCTAATGAAGAG
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
-----gtacctatta---agttgtaaaggaaaaaaaaccataagttgaataggatgagt-ctgtgttat--tgtagtctgaaattgctga------caga-gtcatattctctttaat--ga----------ctgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
| | |||| | | || | || || ||| | | |||| |||| || | | | || || | ||| |||| | || | | || | || || | ||| ||||||||||||| || ||||| |||||||| ||||||||||| || || || || ||| | || || |||||||||||||||| || ||||||||||||
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaagaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 6
gtacctattaagttgtaaaggaaaaaaaaccataagttgaataggatgagtctgtgttattgtagtctgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
||| || || | || | | | | | || |||| |||| || | | | | | || | || | || ||||||||||||||||||||||| ||||||||| |||||||||| || || ||||||||| ||||||| ||||| ||||| || || ||||| || ||||||
--------------gtactcctcaataatttct--cttcgttggtagtaagttaaatt-ttgtc-tctgtaaataactattgtatgagatgaccatt------tattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGGCCTGGACGAATTGACAGGAAGATTGAGTTCCCAAATCCCAACGAAGAG
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------------------------------------gtacctattaagt-tgtaaaggaaaaaaaaccataagttgaataggatgagtctgtgttattgtagtctgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
|| ||||| || ||| | || | | | ||| | || || | |||| | || || | | | | | | || |||||||| |||||||||||||| ||||||||||| || ||||| || |||||||| ||| | ||||| ||||| ||||| ||||| ||||| |||| |||
gtactattaataattgctaccctttttgcttctgctgtagttgtgtgtgcccacttgtattatatttgtgtatttatatgtattatgtgtgtggtatttgttatctagtagaatcagcaaaatggttggaaattggtggaatctgta-----tgtcatatctgtgacaacatgatcaatattttcagGTTTTAATGGCTACAAATCGAATTGATATTCTTGACCAAGCCCTCCTCAGGCCAGGACGGATTGACAGGAAGATTGAGTTTCCAAATCCCAATGGGGAG
upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S7016_1V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacctattaagttgtaaaggaaaaaaaaccataagttgaataggatgagtctgtgttattg--tagtctgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
|| || || | ||| || || | ||| | || | ||||| || | | || || | | | | || | | |||| ||||||| ||||||||||| ||||| ||||||||||| ||||||||||| | | || ||| ||||||| |||||||||| || || ||||| | ||||||
-------ttgggtgagtaa--ataaacaatcacatgttctgaaaattgccttcgtgttgctggttgactttcaactgattatcaacta----cctatcttgggacttatgcagGTGTTGATGGCTACGAATCGAATTGATATTCTAGATCAAGCTCTCTTGCGACCCGGACGAATTGACCGGAAAATTGAGTTCCCCAATCCAACCGAAGAGMapped 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|86084788|gb|DR380547.1|DR380547EST: TCGAGCTTCTCAATCAACTTGACGGTTTTGAAGCGTCAAACAAAATCAAG GTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGG
genomic: TCGAGCTTCTCAATCAACTTGACGGTTTTGAAGCGTCAAACAAAATCAAGgtacctatta ... actgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGG
EST:
gi|164068859|gb|ES123330.1|ES123330EST: TCAACTTGACGGTTTTGAAGCGTCAAACAAAATCAAG GTTTTGATGGCTACAAATCGTATTGATATTCTGGAATACAAGCTCTTCTCA
genomic: TCAACTTGACGGTTTTGAAGCGTCAAACAAAATCAAGgtacctatta ... actgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGA-T-CAAGCTCTTCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattgtagtctgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
atattctctttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctattaagttgtaaaggaaaaaaaaccataagttgaataggatgagtctgtgttattgtagtctgaaattgctgacagagtcatattctctttaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCAGGCCTGGAAGAATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA