Sequence
atgc intronic sequence ATGC exonic sequencegtgagtctctttgaaaacttaacgtttgtgttcttcataaccatttttatctcatgattgttatgtataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAAGTAAGAGAGAAGAAGACTTCAAAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55340.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55340.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G024395_T03 (Zea mays), 3'ss of exon 3
----------------------------gtgagtctctttgaaaacttaacgtttgtgttc-ttcat---aaccatttttatctcatgattgttatgtataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAAGTAAGAGAGAAGAAGACTTCAAAGAAG----------------------
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gtaatgctcccttccactaattcattttataagttttcacttcattgctatgatcgtactcattcatttgaacatgtcttctgttacattttttggaca-actgtagATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAAGTTAGAGAGAAGAAGAGTTCTAAAAAGGTACCCTGCATATAGATATCTT
upper sequence: AT1G55340.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G024395_T02 (Zea mays), 3'ss of exon 3
----------------------------gtgagtctctttgaaaacttaacgtttgtgttc-ttcat---aaccatttttatctcatgattgttatgtataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAAGTAAGAGAGAAGAAGACTTCAAAGAAG
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gtaatgctcccttccactaattcattttataagttttcacttcattgctatgatcgtactcattcatttgaacatgtcttctgttacattttttggaca-actgtagATGGTGAGCCCAGGAGCTTGGTTATCAGATCTATCTCATGAGAGATATGAAGTTAGAGAGAAGAAGAGTTCTAAAAAG
upper sequence: AT1G55340.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G081943_T06 (Zea mays), 3'ss of exon 3
---------------------------gtgagtct---ctttgaaaact-taacgtttgtgttcttcataaccatttttatctcatgattgttatgtataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAAGTAAGAGAGAAGAAGACTTCAAAGAAG
|| ||| | ||| | || | || | | || | | ||| | | | | ||| | | | || ||||||| ||||||||||||||||||||| ||| | |||||||||||||| ||||||||||||| ||| || |||
gtaatgctcactccactgattcagtctgtaagttttcacttccattgctatgaccatgctcatccttttgaccctgccttctgctttatttctggacgaactatagATGGTGAGCCCAGGAGCTTGGTTATCAGATTTGTCGCATGAGAGATATGAAGTTAGAGAGAAGAAGAGTTCTAAAAAG
upper sequence: AT1G55340.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G432560_T03 (Zea mays), 3'ss of exon 1
gtgagtct---ctttgaaaact-taacgtttgtgttcttcataaccatttttatctcatgattgttatgtataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAAGTAAGAGAGAAGAAGACTTCAAAGAAG
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gtaagttttcacttccattgctatgaccatgctcatccttttgaccctgccttctgctttatttctggacgaactatagATGGTGAGCCCAGGAGCTTGGTTATCAGATTTGTCGCATGAGAGATATGAAGTTAGAGAGAAGAAGAGTTCTAAAAAG
upper sequence: AT1G55340.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G432560_T04 (Zea mays), 3'ss of exon 1
----------------------------gtgagtct---ctttgaaaact-taacgtttgtgttcttcataaccatttttatctcatgattgttatgtataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAAGTAAGAGAGAAGAAGACTTCAAAGAAG
|| ||| | ||| | || | || | | || | | ||| | | | | ||| | | | || ||||||| ||||||||||||||||||||| ||| | |||||||||||||| ||||||||||||| ||| || |||
gtaatgctcactcccactgattcagtctgtaagttttcacttccattgctatgaccatgctcatccttttgaccctgccttctgctttatttctggacgaactatagATGGTGAGCCCAGGAGCTTGGTTATCAGATTTGTCGCATGAGAGATATGAAGTTAGAGAGAAGAAGAGTTCTAAAAAG
upper sequence: AT1G55340.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G081943_T09 (Zea mays), 3'ss of exon 3
---------------------------gtgagtct---ctttgaaaact-taacgtttgtgttcttcataaccatttttatctcatgattgttatgtataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAAGTAAGAGAGAAGAAGACTTCAAAGAAG----------------------
|| ||| | ||| | || | || | | || | | ||| | | | | ||| | | | || ||||||| ||||||||||||||||||||| ||| | |||||||||||||| ||||||||||||| ||| || |||
gtaatgctcactccactgattcagtctgtaagttttcacttccattgctatgaccatgctcatccttttgaccctgccttctgctttatttctggacgaactatagATGGTGAGCCCAGGAGCTTGGTTATCAGATTTGTCGCATGAGAGATATGAAGTTAGAGAGAAGAAGAGTTCTAAAAAGGTAGCCTGCATTTAGATATATT
upper sequence: AT1G55340.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g00430.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------gtgagtctctttgaaaacttaacgtttgtgttcttcataaccatttttatctcatgattgttatgtataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAAGTAAGAGAGAAGAAGACTTCAAAGAAG
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gtaagtaatttttttcctatttcctctttaaattcacagaaagacaaaatcagagaaaatagaggttttgagaagaaatttcagtttttgtgatgtgggtgtgtgttgatttgattcctctgat-tgttgtgcagTTGGTGAGTCCAGGTGCATGGCTATCAGACCTGTGCCAAGAGAGGTATGAAGTGAGGGAGAAGAAGGCTTCCAAGAAGMapped 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|164110780|gb|ES063681.1|ES063681EST: GGTTCAGAAGACATTGCTT CTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAA
genomic: GGTTCAGAAGACATTGCTTgtgagtctct ... tataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacgtttgtgttcttcataaccatttttatctcatgattgttatgtataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAAGTAAGAGAGAAGAAGACTTCAAAGAAG
tcataac putative branch site (score: 2)
attgttatgtataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtctctttgaaaacttaacgtttgtgttcttcataaccatttttatctcatgattgttatgtataatgcagCTGGTGAGTCCAGGAGCTTGGTTATCAGATCTGTGCAAAGAGAGATATGAAGTAAGAGAGAAGAAGACTTCAAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG