Sequence
atgc intronic sequence ATGC exonic sequence...gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42990.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 4
-gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
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ctctgtgattgtgaaccaaaagagagatgagatacagtttttatgcataaatataatggccat-taagaataacagcttgctgctggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAG
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 4
-gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG-----------
| || || || | | || ||| | | || | | || | | | | || | | || |||||| |||||||| || ||||| || |||||||| || ||||| |||||||||||||| | |||||| | |||||||| || | ||||
ctctgtgattgtgaaccaaaagagagatgagatacagtttttatgcataaatataatggccat-taagaataacagcttgctgctggtcatatatctgcagATATACTGTATGATTCTTGGTCACCTGCAATGACTGTCAGTTCGGTCTGCATCAGCATTTTGTCAATGTTGTCAAGTTCACCAGCAAAGGTTATTATATA
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 4
--gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
| | | | | | || || | | | | ||| | | | || || | | | ||| || || | | || ||||||| |||||||||| ||||||||||| ||||| ||||| || ||||| ||||| ||||| || ||| | || ||||| || | ||||
gaatggaaggaaaacaatgttggtgtagccttgatggccatggactacagtttact-gtatgatttg-tgattatcggctttctgctgcctcttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 4
gttacaatacataatcacgattatacccggcctcattttaggagaa----agtccatta-ggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
| || ||| || || | |||| | | | | | ||| | | | || | |||| | || | || | | || | | || |||||||||||||||||| ||||| ||||| ||||| ||||| || ||||| ||||| ||||| || ||| | || ||||| || | ||||
---atggaacgtaaaca-atttttgtggagccttgatggatgtggattacagtttactgtatggtttgtgattaaca-aattcctgctgttactcttgtctgcagATATTCTGTATGACTCGTGGTCACCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G07810.1 (Glycine max), 3'ss of exon 4
gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattc-ctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
|||| | | | ||| | | | | | | || || || | | | ||| | | || | | || |||||| ||||||| ||||||||||| || |||||||| ||||| |||||||||| || ||||||||||| ||||| || || ||||
gtta-gccatttttttctttttaaatttagatgaaagcgtgattgacttggtactggtttttgatggtgagctgacatttaatgtgcttggcatcatgcagATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G07810.2 (Glycine max), 3'ss of exon 4
gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattc-ctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG--
|||| | | | ||| | | | | | | || || || | | | ||| | | || | | || |||||| ||||||| ||||||||||| || |||||||| ||||| |||||||||| || ||||||||||| ||||| || || ||||
gtta-gccatttttttctttttaaatttagatgaaagcgtgattgacttggtactggtttttgatggtgagctgacatttaatgtgcttggcatcatgcagATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGGT
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
gttacaatacataatcacgattatacccggcctcattttaggagaaagtccat-taggattatgcgcttaatataacacactctctaattc-ctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
|||| | | | | ||| | | | | | || | | | | || || || | | | ||| | | || | | || |||||| ||||||| |||||||| || || |||||||| ||||| |||||||||| || ||||||||||| ||||| || || ||||
gtta-accatttttttctttttaaatttaga-taaaagcatgattgacttggtgttggtttttggtggtgagctgacatttgatgtgcttgacatcatgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 4
gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattcctttttgt------agATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
| | | ||| | || | || || | | | | || ||| | | | ||| | | || || ||| ||| ||||||| |||||| |||||||||| ||||| ||||||||||| ||||| || ||||||||||||||||||| ||| |||| ||||| | | |||
----aatcatagaatgaaga--acactcgacgcagtcatgagggagagtggtgcacgttaatgaaatgatgatttttcattctgggatttatttttgttcaaccagATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAG
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
----gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggatta--tgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
||| | | || ||| | | ||| | | | | | | | || | ||| | | |||| | || || ||| ||| ||||||||| |||||||| ||||| ||||||||||| |||||||| |||||||||||||||| || ||| | || ||||| | | |||
acgagttccca-acttaacgaaaactatctctg----tgtacttgaatttaacatgttgcgtttaattaagactaatttc-tgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ21480 (Selaginella moellendorffii), 3'ss of exon 4
--gttacaatacataatcacgattatacccggcctcattttag--gagaaagtccatta-ggattatgcgcttaa-tataacacactctctaat-----tcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
| | | | || | | || | || | || || | | | |||| || || || | || ||| | ||||| | ||||||||| ||||| || ||||| ||||| ||||| || || || ||||||||||||||||||| ||||| || || ||| | | |||
gtgaagctttctctctctctcttttttttttacttctctccagccgtgatagatcttgatggatgatcgactcaaacttttcatttcttcttgtgtgtgtccttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ27071 (Selaginella moellendorffii), 3'ss of exon 4
gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
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---------gtgaacctttcttctctccagccttgatagatcttgatggatgattgactcaaacttttcatttctt---ttgtgtgtgttcttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGMapped 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|124923748|gb|EL001907.1|EL001907EST: ACCAGCACCGTTACATCCTCATATTTACAGCAATGGACATATTTGTTTAG ATATTCTGTATGACTCATGGTTTCCAGCAATGACAGTG
genomic: ACCAGCACCGTTACATCCTCATATTTACAGCAATGGACATATTTGTTTAGgtaattttac ... ctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtccattaggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
ctctaat putative branch site (score: 3)
ctctctaattcctttt CT-rich tract
ttaatataaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG
- - caataca
- - - - - - - - - - - - - - - - - - - - ggagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tataaca