Sequence
atgc intronic sequence ATGC exonic sequencegtaacatcctaagctttagtttttcatgtttccttgtgcttcaagtttgtgtaaccattgtagctaattctttggggttttggttgaaataaagGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01480.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 6
--gtaacatcctaagctttagtttttcatgtttccttgtgcttcaagtttgtgtaac-cattgtagctaattctttgggg---ttttggttgaaat---aaagGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA
| ||| | | | || || |||| ||||| || || ||| | | |||| | | || ||| | || | ||| || ||||||||| |||||||| |||||||| || ||||| ||||||||||| |||| ||| ||| | | |||| || || ||||||| || ||| ||||||
gcatgacaacttcattcttttttggcagagttttattgtga---aaattgctgtctcactttgttgttgatctaatggtgcacttgtttttggaacataaaagGGTGAGAAAGATGATAAGATCATCGCGGTTTGCGTTGATGATCCCGAGTTCCGCCACTTCAATGATCTCAAGGAGCTCTCTCCTCACCGACTTGCTGAAA
upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
gta-acatcctaagctttagttttt--catgtttccttgtgctt---caagtttgtgtaaccattgtagctaattctttgg----ggttttggttgaaataa--agGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA
||| | | ||| || |||| | || | | | ||| | | | | || ||| | | |||| | | | ||||||| || ||||||||||| || ||||| |||| |||||||||||| || || || | |||||| ||| || ||||||| || || || |
gtatattttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
-----------------gtaacatcctaagctttagtttttcatgtttccttgtgcttcaagtttgtgtaaccattgtagctaattctttggggttttggttgaaataaagGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA
||| || | | | | ||| || || ||||| | || | || | | | || ||||| ||| ||||||| || ||||||||||| || ||||| |||| |||||||||||| || || || | |||||| ||| || ||||||| || || || |
tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactc---tttttgttttgttt---tttttttactgacgatattggattttg--tgatc---agGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA
upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G015418_T01 (Zea mays), 3'ss of exon 6
gtaacatcctaagctttagtttttcatgtttccttgtgcttcaagtttgtgtaac-cattgtagctaattctttggggttttggtt--gaaataa--agGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA
| | | | || | ||| || | | | || | |||| | ||| | | | || || | ||||| ||||||| |||||||| ||||| ||||||||||||||||| ||||||||||| ||| | || | |||| || ||| |||| || || ||| |||||
--------gcatgatgcgtctattgacacttcattagaactagcttgtacatatcgcattatgttggattgatggcacatctgtttctgcaataactagGGTGAGAAAGATGATAAGATAATTGCAGTTTGTGTTGACGATCCTGAGTACCGCCACTTAACCGATCTCAAGGAGCTTTCTCCGCACCGCCTTAATGAAA
upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 6
gtaacatcctaagcttta-gtttttcatgtttccttgtgcttcaagtttgtgtaaccattgtagctaattctttggggttttggttgaaataa--agGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA
|| | ||| | | || | | | | | | || | | | | | || ||| | || | | | |||||||||| ||||||||||| || ||||| |||| |||||||||||| ||| ||| || |||||| ||| || |||||||||| || || |
---gtatttcacgctagacactatttgaggtagagggaaaagaatgactctgctttgactctgtttcaaactatggctatctgttgggcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA
upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 6
gtaacatcctaagctttagttt--ttcatgtttccttgtgcttcaagtttgtgtaacca-ttgtagctaattctttggggttttggttgaaataa--agGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA
|| | | | || | || || | | | | || | | |||| |||| | |||| || || | | | |||||||||| ||||||||||| || ||||| |||| |||||||||||| || ||| || |||||| || || ||||||| || || || |
---gtatttcatgttacagctctatttgtggtagagggaatagaagagctctgcttcgacttgtttctaa--ccttggatttctgttgggcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCACTACAACGACATCAGCGAGCTGTCTCCTCACCGCCTGCAAGAGAMapped 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|116470399|gb|EG512991.1|EG512991EST: GTTGTTTTCTTCGCGCCCGAGCTATTGGTTTAATGCCTATGATTGACCAG GGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGAT
genomic: GTTGTTTTCTTCGCGCCCGAGCTATTGGTTTAATGCCTATGATTGACCAGgtaacatcct ... tgaaataaagGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGAT
EST:
gi|116470397|gb|EG512989.1|EG512989EST: GTTGTTTTCTTCGCGCCCGAGCTATTGGTTTAATGCCTATGATTGACCAG GGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGAT
genomic: GTTGTTTTCTTCGCGCCCGAGCTATTGGTTTAATGCCTATGATTGACCAGgtaacatcct ... tgaaataaagGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaagtttgtgtaaccattgtagctaattctttggggttttggttgaaataaagGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA
agctaat putative branch site (score: 3)
ttgaaataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatcctaagctttagtttttcatgtttccttgtgcttcaagtttgtgtaaccattgtagctaattctttggggttttggttgaaataaagGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC