Sequence
atgc intronic sequence ATGC exonic sequencegtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22140.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
-------------------------------gtaagtagataaatagta-atcagatcagaa-ctacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
| || ||| | || | ||| | | | | ||| | | || | || | | | ||| | || || | |||||||| |||||||| ||||| ||||| ||||| || || ||||||||||||||||| || | |||||| |||||
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
-----------------------gtaag---tagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttggt-tctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
|||| | | | | || | | ||||| || || | | | ||||||| |||| |||| ||||| || | ||||| || ||||| ||||| ||||| ||||| || || || |||||||||||||||||||| ||||| |||||
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggtta-atcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtga--cattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G091265_T05 (Zea mays), 3'ss of exon 2
---------------------gtaag---tagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttggt-tctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
|||| | | | | || | | ||||| || || | | | ||||||| |||| |||| ||||| || | ||||| || ||||| ||||| ||||| ||||| || || || |||||||||||||||||||| ||||| |||||
gtacaaagctcttccttttctgtaaccttttgtcatgtggtggtta-atcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtga--cattgtttgtatgtgaagATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G119357_T01 (Zea mays), 3'ss of exon 2
gtaagtagataaatagtaatcagatcag-aactacgccttcttattacctggaatttccatg-attttttatctgttgtgggt-tgttgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
||| | || | | | | || ||| ||||| | | || ||| || | || ||| | || ||| || ||| |||||| ||||||||||| ||||| ||||| || || || |||||||||||||| |||| ||||| |||||
gtacggagctcctcaatcctttcattgttgactttttcttctctgtgcatgcgttttgagcctgcttgtgataatttgggtgtgtgtatttttctctaaagGTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgt-tgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
||| | || | | | || || | ||| | || | || || | |||||||| | || ||| |||||| ||||||||||| ||||| ||||| || || || |||||||||||||| || | ||||| ||||
gtatgaagctcctcaacccttccattgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggttgtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttg--ttg-gttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
|| | | | | |||| | || | | || || | | | | | | | || ||| ||| ||| |||||||| ||||||||||| |||||||| || || || ||||||||||| || |||||||| ||||| || ||
-ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatct--gttgtgggttgttgttggt--tctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
|| || || || | | | || | | || ||| | | ||| || ||| | |||| ||| || | |||||||| ||||||||||| |||||||| || || || ||||||||||| || |||||||| ||||| || ||
--gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
gtaagtagataaata-------gtaatcagatcagaac----tacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttg-gttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
|||||| | || || | |||| | | | || | | | || ||| || ||| || | | | ||| | ||| ||| |||||||| ||||| || || |||||||| || ||||| || ||||||||||||||||| || ||||| || ||
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G34740.3 (Glycine max), 3'ss of exon 2
gtaagtagataaatag-------taatcagatcagaac----tacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttg-gttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG-------------------------------
|||||| | || || | |||| | | | || | | | || ||| || ||| || | | | ||| | ||| ||| |||||||| ||||| || || |||||||| || ||||| || ||||||||||||||||| || ||||| || ||
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGGTAAAACCAGTATATTCTGCTTTTTTTTGTT
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttg-gttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
|||||| || | | | | | | | || | | | || ||| || ||| || | ||| | | | ||| | | |||||||| ||||| || || |||||||| || ||||| || ||||||||||||||||| || ||||| || ||
gtaagtttatttctgttttttttagtgagataatg--ttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S56_182V6.1 (Physcomitrella patens), 3'ss of exon 2
-gtaagtagataaatagtaatcagatca-gaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttggt-tctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
| | | | |||| | || ||| | ||||| || ||| || | ||| | ||| | |||| | || || || ||||| ||||||||||| |||||||| ||||| | ||||| || |||||| ||||||||||||
cgattttggctttgtagttacatcttcctgaaagatgccttaa-atagaaaacaatccttgtgccgtattagtaatcgtgaccttcaactggtgtatgcagTTATTGCAAGTGTGAAATGCCATACAATCCTGACGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ05369 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
| |||| || | || ||| | | |||| | || || | | | ||| || | || | ||| | | ||||||||||| || || ||||||||||| || || ||||| |||||||||||||| | |||||||||||
------------------gtaagattg--acaaagc--tctcact--ttggattctctatcttatgctctctttttttgggt-ttgcggaaac---agGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
--gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttat-ctgttgtgggttgttgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
| | | | | || || || | || || | | | | || | | | || | | || | | | |||||||| ||||||||||| ||||| |||||||| |||||| | ||||| ||||| || |||||| || ||
gtctcgttgtgttcgaacttctctt-tcctctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
upper sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ26805 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
| |||| || | || ||| | | |||| | || || | | | ||| || | || | ||| | ||||||||||| || || ||||||||||| || || ||||| |||||||||||||| | |||||||||||
------------------gtaagattg--acaaagc--tctcact--ttggattctctatcttatgctctctttttttgggt----ttgaaac---agGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGMapped 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|124981359|gb|EL054233.1|EL054233EST: CGCATTTACCCCTGATCGAGTTGCTGTT GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGT
genomic: CGCATTTACCCCTGATCGAGTTGCTG-Tgtaagtagat ... ggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacctggaatttccatgattttttatctgttgtgggttgttgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
atgattttttatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG