Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgaaaattacttgtatgtatattcattgtgggaaaaatcatcgtactacagagggtattgtctaactgttgtgatttttctgaattgagtttagATACTTTCTACTGGACTTGGTAGGATAGTGCCAAACTTGATATCGAGGAAGCACACCAATAGTGCTGCTACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G36290.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G36290.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g28300.1 (Oryza sativa), 3'ss of exon 4
gtaagttgaaaat-tacttgtatgtatattcattgtgggaaaaatcatcgtactacagagggtattgtcta-actgttgtgatttttctgaattgagtttagATACTTTCTACTGGACTTGGTAGGATAGTGCCAAACTTGATATCGAGGAAGCACACCAATAGTGCTGCTACAG
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atgtttggtatatgtatatgccaattatttaatttcatttaatcttataagaaattacatgggtttgtatatgctgttaatatgtatatttgttc--tcaagGTACTATCAACTGGACTTGGTAGGATAGTCCCCAACTTGATATCAAGGAAGCACACTAACAGTGCTGCTACAG
upper sequence: AT5G36290.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 4
gtaagttgaaaattacttgtatgtatattc---attgtgggaaaaatcatcgtactacagagggtattgtctaactgttgtgatttttctgaattgagtttagATACTTTCTACTGGACTTGGTAGGATAGTGCCAAACTTGATATCGAGGAAGCACACCAATAGTGCTGCTACAG
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-tctatgccaaattctttgtttttatagtctaagctgttgccacaatttttttttgattctctatgctgcttacatatt-tgcccaccctctccccaaca-agGTATTGTCAACTGGACTTGGCAGAATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAG
upper sequence: AT5G36290.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G47670.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------gtaagttgaaaattacttgtatgtatattcattgtgggaaaaatcatcgtactacagagggtattgtctaactgttgtgatttttc-------------------tgaattgagt-----------ttagATACTTTCTACTGGACTTGGTAGGATAGTGCCAAACTTGATATCGAGGAAGCACACCAATAGTGCTGCTACAG
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gtaagtgcaacatgggatgcatttttggttttaatatttctgcattgttgtttctcattattggatgtactttt-tgtgttgttgtgatggaatggtttgcgcaactacagagcactatttctgggtgctctaacttttcatattaatgttatcaggattaaagttactgtacgtgtcaattagGTACTTTCTACAGGGCTTGGCAGGATTGTGCCAAATTTGATTTCTAGGAAGCATACGAATAGTGCTGCTACAG
upper sequence: AT5G36290.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G38640.1 (Glycine max), 3'ss of exon 4
gtaagttgaaaattacttgtatgtat----attcattgtgggaaaa--atcatcgtactacagagggtattgtctaactgttgtgatttttctgaattgagtttagATACTTTCTACTGGACTTGGTAGGATAGTGCCAAACTTGATATCGAGGAAGCACACCAATAGTGCTGCTACAG
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------agagcactatttctgggtgctctaactcttcatattaatgttatcaggatactgataaaaaaaaattatcaggattaaatttattgtacgtgtcaattagGTACTTTCTACAGGGCTTGGCAGGATTGTGCCTAATTTGATTTCTAGGAAGCATACAAATAGTGCTGCTACAGMapped 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|164076213|gb|ES212000.1|ES212000EST: CTCTCAGCTTTGTTTGTTATGACT ATACTTTCTACTGGACTTGGTAGGATAGTGCCAAACTTGATATCGAGGAAG
genomic: CTCTCAGCTTTGTTTGTTATGACTgtaagttgaa ... ttgagtttagATACTTTCTACTGGACTTGGTAGGATAGTGCCAAACTTGATATCGAGGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcgtactacagagggtattgtctaactgttgtgatttttctgaattgagtttagATACTTTCTACTGGACTTGGTAGGATAGTGCCAAACTTGATATCGAGGAAGCACACCAATAGTGCTGCTACAG
gtctaac putative branch site (score: 2)
tgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgaaaattacttgtatgtatattcattgtgggaaaaatcatcgtactacagagggtattgtctaactgttgtgatttttctgaattgagtttagATACTTTCTACTGGACTTGGTAGGATAGTGCCAAACTTGATATCGAGGAAGCACACCAATAGTGCTGCTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT