Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgcatgttagatacacatcgaaattctttggttggctatcctctgttaaagcagttgagctcgtgctctcctagctgtttaaataattccggctatctcccagcaaccaagatgtgctaaattgtcttcattctcttgtgagtaaaacattataattgcataagcactgacaatttatgaccatcagGTTGATGCAAAGGGCGGATTGTCAAAGAAATTGTTTGACTTTGCATATGCTCGGCGATTATCTGCAATCAATGGAAGTTGGTTTGGAGCCTGGGGATTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G77590.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 1
gtttgtgcatgttagatacacatcgaaattctttggttggctatcctctgttaaagcagttgagctcgtgctctcctagctgtttaaataattccggctatctcccagcaaccaagatgtgctaaattgtcttc--attctcttgtgagtaaaacattataattgcataagcactgacaatttatgaccatcagGTTGATGCAAAGGGCGGATTGTCAAAGAAATTGTTTGACTTTGCATATGCTCGGCGATTATCTGCAATCAATGGAAGTTGGTTTGGAGCCTGGGGATTGG
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-----------------------------------------------------------------------------------------------gtattgttctttacaatgatattatccattgtttctttctggccttcttgccatcttgaccatttgtttttttca----tgatgag--atga--attagGTTGATGCAAAGGGTGGTGCAGCAAAGAAACTATTTGATATTGCCTATAGCCGTCGGTTAGCTGCTATCAATGGAAGTTGGTTTGGTGCATGGGGATTAG
upper sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 6
gtttgtgcatgttagatacacatcgaaattctttggttggctatcctctgttaaagcagttgagctcgtgctctcctagctgtttaaataattccggctatctcccagcaaccaagatgtgctaaattgtcttcattctcttgtgagtaaaacattataattgcataagcactgacaatttatgaccatcagGTTGATGCAAAGGGCGGATTGTCAAAGAAATTGTTTGACTTTGCATATGCTCGGCGATTATCTGCAATCAATGGAAGTTGGTTTGGAGCCTGGGGATTGG
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---------------------------------------------------------------------------------------------------------------gtaatgtccttcacattgttctggtccagt-gtaccttgctgattattgacagctaccttttgtgttgagatgtct-tcagGTGGATACAAAGGGTGGTATAGCAAAGCAATTGTTTGACATTGCCTATAACCGTCGGCTTGCTGCAATCAATGGAAGTTGGCTTGGTGCCTGGGGACTGG
upper sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 7
gtttgtgcatgttagatacacatcgaaattctttggttggctatcctctgttaaagcagttgagctcgtgctctcctagctgtttaaataattccggctatctcccagcaaccaagatgtgctaaattgtcttcattctcttgtgagtaaaacattataattgcataagcactgacaatttatgac-catcagGTTGATGCAAAGGGCGGATTGTCAAAGAAATTGTTTGACTTTGCATATGCTCGGCGATTATCTGCAATCAATGGAAGTTGGTTTGGAGCCTGGGGATTGG
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gtttgtgaattttgg-catgcataagaa---tatacatatgcatacatattcatatctgc-aagcatgcatagttattattatt-atatattttggtgtgtatttgagaa---------tgttgaatt------------tgatgtctgatacaaggtgattacataaataatgaattttgttaacacttcagGTAGATGCAAAGGGTGGTCTAGCCAAGAAATTGTTTGATTTAGCATATGCACGTAGGTTGTCAGCAATCAATGGCAGTTGGTTTGGGGCTTGGGGTCTAGMapped 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|19875635|gb|AU236466.1|AU236466EST: CAGCTGTTCCAGCCATTCTTGATCGTGTCAGGGATGGTGTCCGCAAAAAG GTTGATGCAAAGGGCGGATTGTCAAAGAAATTGTTTGACTTTGCATATGCT
genomic: CAGCTGTTCCAGCCATTCTTGATCGTGTCAGGGATGGTGTCCGCAAAAAGgtttgtgcat ... tgaccatcagGTTGATGCAAAGGGCGGATTGTCAAAGAAATTGTTTGACTTTGCATATGCT
EST:
gi|163986148|gb|ES186254.1|ES186254EST: CAGCTGTTCCAGCCATTCTTGATCGTGTCAGGGATGGTGTCCGCAAAAAG GTTGATAGACAAAGGGCGGATTGTCAAAGAAATTGTTTGACTTT
genomic: CAGCTGTTCCAGCCATTCTTGATCGTGTCAGGGATGGTGTCCGCAAAAAGgtttgtgcat ... tgaccatcagGTTGAT-G-CAAAGGGCGGATTGTCAAAGAAATTGTTTGACTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttgtgagtaaaacattataattgcataagcactgacaatttatgaccatcagGTTGATGCAAAGGGCGGATTGTCAAAGAAATTGTTTGACTTTGCATATGCTCGGCGATTATCTGCAATCAATGGAAGTTGGTTTGGAGCCTGGGGATTGG
cactgac putative branch site (score: 2)
taaaacattataattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgcatgttagatacacatcgaaattctttggttggctatcctctgttaaagcagttgagctcgtgctctcctagctgtttaaataattccggctatctcccagcaaccaagatgtgctaaattgtcttcattctcttgtgagtaaaacattataattgcataagcactgacaatttatgaccatcagGTTGATGCAAAGGGCGGATTGTCAAAGAAATTGTTTGACTTTGCATATGCTCGGCGATTATCTGCAATCAATGGAAGTTGGTTTGGAGCCTGGGGATTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG