Sequence
atgc intronic sequence ATGC exonic sequencegtgagtctgcaacaacaaggttgattatcaatgtttaactcggggtcagatgggataaaatgattgagaaacacttgtattgtagATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTTCTCAAGACACTAATCGAAAAAACTTTAAGAGAAAGGCAAGACTCAGTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22400.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g05540.1 (Oryza sativa), 3'ss of exon 4
gtgagtctgcaaca-acaaggttgattatcaatgtttaactcggggtcagatgggataaaatgattgagaaacacttgtattgtagATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTTCTCAAGACACTAATCGAAAAAACTTTAAGAGAAAGGCAAGACTC-AGTGG
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--------gtaatgcactgtcctaataataaacttatgattttaagtgtggtcgatgcttactgtcatgca-catatgtaatgcagATGTCAGATCCATTGACCGCACTGATGTATGCGGTGCAAGTGATGAATTTTCTCAAGATGCTAATACAGAAGACCCTCAAGGGTAGACAAGAGTCCAATC-
upper sequence: AT5G22400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
-------------gtgagtctgcaacaacaaggttgattatcaatgtttaactcggggtcag--atgggataaa-atgattgagaa--------acacttgtattgtagATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTTCTCAAGACACTAATCGAAAAAACTTTAAGAGAAAGGCAAGACTCAGTGG
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gtattgcattgtgctaatattgtagcaattag-caaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
upper sequence: AT5G22400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G113073_T01 (Zea mays), 3'ss of exon 4
----------gtgagtctgcaacaacaa--ggttgattatcaatgtttaactcggggtcagatgggataaaa-tgattgagaaacacttgtattgtagATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTTCTCAAGACACTAATCGAAAAAACTTTAAGAGAAAGGCAAGACTCAGTGG
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gtattgcattgtgctgatacgatagcgattagcaaactatcaatatatacttca---cccatcacaatgatgctaactatagcacgcttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCGACCC
upper sequence: AT5G22400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S159_36V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------------gtgagtctgca-acaacaaggttgattatcaatgtttaactcggggtcagatgggataaaatgattgagaaacacttgta--ttgtagATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTTCTCAAGACACTAATCGAAAAAACTTTAAGAGAAAGGCAAGACTCAGTGG
| | | | | | ||| |||| | || | | || | || || ||| | | | | | ||| |||||| ||| ||| |||||||||||||| |||| |||||||| ||||| || ||||| || || || ||| | | || || | | ||| ||
gtatgtgatgtcgctgcaattgtgcgcctccccaaacttgtgacacttttcttaccagacttgtagagattcggtcctgtagttagcagactctccgactagatttctacgtgatctaaggaagtatttgtgttaagcttgttatatgaagtgaataacatattaactatgattcattacttgcagATGGCTGACCCATTGACAGCACTGATGCATGCTGTTCAAGTTATGAATTTGCTCAAAACTCTGATTCTCCGCACTCTCAAGGACCGGAAGGCCTCGCTGC
upper sequence: AT5G22400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------------------------gtgagtctgcaacaacaaggttgattatca--atgtttaactcggggtcagatgggataaaatgattgagaaacact---tgtattgtagATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTTCTCAAGACACTAATCGAAAAAACTTTAAGAGAAAGGCAAGACTCAGTGG
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gtatagtgttgtttctacgcttttcacccagagaagctgatgaccattacaagatcagactcgtagagatttcactacagatgctgtcttcgacgtttcatgtgctgaatttgaacgtaggtattccgtgtttatggtgtttcaattgttgtagaatgtgtaacatttattgacattgcttcattatccttcagATGGCTGATCCACTGACAGCTCTGATGCATGCTGTTCAAGTCATGAACTTGCTCAAAACTCTGATTCTTCGCACACTGAAGGACCGAAAGGCCACTTTGCMapped 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|47830354|gb|CK120038.1|CK120038EST: AGATGAATTCACGCAACATCGCTATGGTTTTCGCACCAAATATGACACAG ATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTT
genomic: AGATGAATTCACGCAACATCGCTATGGTTTTCGCACCAAATATGACACAGgtgagtctgc ... tgtattgtagATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtttaactcggggtcagatgggataaaatgattgagaaacacttgtattgtagATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTTCTCAAGACACTAATCGAAAAAACTTTAAGAGAAAGGCAAGACTCAGTGG
gtttaac putative branch site (score: 3)
ataaaatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtctgcaacaacaaggttgattatcaatgtttaactcggggtcagatgggataaaatgattgagaaacacttgtattgtagATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTTCTCAAGACACTAATCGAAAAAACTTTAAGAGAAAGGCAAGACTCAGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA