Sequence
atgc intronic sequence ATGC exonic sequencegtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43810.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatac---tcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
|||||| | | || || ||| || | |||| || || || | | | | | | | | | |||||||||| |||||||||||||| ||||| ||||| ||||| || || || |||||||| ||||| ||||||| || || |||||| | || || ||||
gtaaggctga-gcatttctat-ggttacatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
----------------------------gtaaggattatacacttttatcaagtagtgga-gcatcgaaattcattat--actcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
| | | || || |||||| || | | || || | ||| | | | || | || | ||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| || ||| ||||||| || || || || | || |||||||
gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggactta-tctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 14
----------------------------gtaaggattata-cacttttatcaagtagtggagcatcgaaattcat----tatactcagtttttttcttttgttttctt-tagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
| | | ||| ||| || |||| | || | |||| ||| | ||| | | | | | | | | | || ||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| || ||| ||||||| || || ||||| | || |||||||
gtaaggctcgttactactttgccatttcttcatcaatatgtcacattcatcaggatatgca-catccttatttttgttccgaacttatctgtctgcctctttctgctcacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAAGACCTTTACAAAACAT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
---------------gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttctt----ttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
| | || | ||| || | | ||| || ||| | | || | | | | | ||| ||| |||||||| || ||||||||||||||||||||||| |||||||| |||||||| |||||||||||||| || || ||||| |||||||||||||| |||| |
gtacacttatgatccatttgtcttg-attttttaatattgcaatggttca-cgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 15
------gtaaggattatacacttttatcaagtagtggagcat--cgaaattcattata--ctcagtttttttcttttgttt------tctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
| |||| | ||||| || | ||||| ||| | ||||| | | | | ||||| ||| ||||| || || || || |||||||| ||||||||||||||||| |||||||| |||||||||||||| ||||| |||||||||||||||||||| ||||| |
gtatttttctaatttatttatctttattt-gttttatagcattgcgatagtcattgagggttttggaaactgataatgtttacccaatctatagGTAGTCGCATCCCAGGACTGGCCCGAAGTGACAAAATATGCCGGTTTAGTATGTGCTCAAGCTCATAGGCAGGAACTTATACAAGATTTGTACAAAACTT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 6
gtaagg--attatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
||| | || || || || | | | | | | | | | | | | | || | | | |||| || || |||||||||||||||||| ||||||||||||| |||||||| |||||||||||||| || || ||||| |||||||||||||| |||| |
gtacgcttatgatccatttgtcttgattttttaattttgcagtggttcttgagctgatatctatcgctcaatacgt--agGTAGTAGCATCTCAAGACTGGCCTGAACTGACAAAATATGCTGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 15
------gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttt-----tttcttttgttt------tctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
| |||| | ||||| || | ||||| | ||| | || ||||| | | ||||| ||| |||| || || || || |||||||| ||||||||||||||||| ||||| || || || |||||||| ||||| |||||||||||||||||||| ||||| |
gtacttatctaatttatttatctttattt-gttttatagcattgcaata-gtcatcgagggttttggaaactcataatgtttacccaatctacagGTAGTAGCATCCCAGGACTGGCCCGAAGTGACAAAATATGCCGGTTTGGTATGCGCCCAAGCTCATAGGCAGGAACTTATACAAGATTTGTACAAAACTT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 12
gtaaggattataca-cttttatcaag--tagtggagcatcg--------aaattcattat------actcagttttt------ttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
|||| || | | || ||||| | | | || | | | ||| | |||| ||| ||| | || || | || | ||||| || |||||||| |||||||||||||| ||||||||||| || || ||||||||||| |||||||| || ||||| ||||||||||| || || ||||
gtaaaatttctttaactgatatcatgcttcctagaaccttgtttttcctaaagtggttattgaggaactttgttgctgatagattgttgtattaattgtagGTAGTAGCTTCTCAGGACTGGCCTGAAGTCACAAAATATGCAGGATTGGTTTGTGCTCAGGCTCACAGACAGGAACTGATACAAGATTTATACAAGACAT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 15
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
||| || || | | | | | || || ||| | | | ||||||||||| || ||||| ||||| || ||||| || |||||||| ||||||||||||||||| || | |||||||| ||||||||| | || || || |
------------------------gta-tgctgctct----tccgctgcagcc-gtgaaactcaattgctgt-tatagGTTGTTGCATCGCAAGATTGGCCCGAGGTGACGAAGTATGCGGGATTAGTTTGTGCTCAAGCACATCGTCAAGAACTGATACAAGATCTCTACAAGACCT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 14
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttctt--ttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
|| ||| || || | | || | | | || | | ||||||| |||||||| || ||||| ||||| || ||||| || ||| |||| || |||||||||||||| ||||| | || |||||||||||||||||||
---------------------------gtaagtgtacgatttttcttttcgtgtgtctctcaataagctgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTAACGAAATACGCAGGTCTAGTCTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATTTGTATAAAACAT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 15
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
||| || || | | | || | || || || ||| | | | ||||||||||| || ||||| ||||| || ||||| || |||||||| ||||||||||||||||| || | |||||||| ||||||||| | || || || |
------------------------gta-tgctgcttt----tccgctacagtc-gtgaaactcaattgctgt-tatagGTTGTTGCATCGCAAGATTGGCCCGAGGTGACGAAGTATGCGGGATTAGTTTGTGCTCAAGCACATCGTCAAGAACTGATACAAGATCTCTACAAGACCT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttct----tttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
|| ||| || || | | || | | | | || | | ||||||| |||||||| || ||||| ||||| || ||||| || ||| |||| || |||||||||||||| ||||| | || |||||| ||||||||||||
---------------------------gtaagtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 14
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttctt--ttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT---------------
| | ||| || || | | || | | | || | | |||||| |||||||| || ||||| ||||| || ||||| || ||| |||| || |||||||||||||| ||||| | || |||||||||||||||||||
--------------------------------gta-cgatttttcttttcgtgtgtctctaaataagctgcctgttaccggttgtcgcttctcagGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATTTGTATAAAACATGGGTTGATCCTCAGAMapped 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|47828868|gb|CK118552.1|CK118552EST: ACGTGACTCACCCAGAGAACGGGGAAGAGTCAAGCCCTTCAATCGCTGCT GTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTT
genomic: ACGTGACTCACCCAGAGAACGGGGAAGAGTCAAGCCCTTCAATCGCTGCTgtaaggatta ... ttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
tactcagtttttttct CT-rich tract
tttttttcttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC