Sequence
atgc intronic sequence ATGC exonic sequence...ttgctaaatatcttgttcaatgactgatttcttaaactcagggtggaaattctgccatggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G27650.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g47750.1 (Oryza sativa), 3'ss of exon 3
ttgctaaatatcttgttcaatgactgatttcttaaactcagggtggaaattctgccatggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT------------------------------------------------------------------------
|| || || || |||||| ||||| || |||||||| |||||||| |||||||| | || || ||||| || |||||||||||||| |||||||||||||| || |||||||| ||||||| ||| | || ||||| || ||||| | | ||
-----------------------------------gttc---gttgattttgaatcatggcagagcacttagcttcaatatttggtacagagaaagataaggtcaactgcccattttacttcaagattggggcttgccgtcatggggatcggtgctcttgtcttcataacagGCCCACCATATCACCAACTGTTGTGTTTGCGAACATGTATCAGCGCCCTGATATGATCACGCCCGGGGTTGATGCTCAAGGCCAGCCGATAGATCCCCGC
upper sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
-ttgctaaatatcttgttcaatgactgatttcttaaactcagggtggaaattctgccat---ggcggagcatttggcttcaatcttt--ggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT-
|| | | ||| |||| || || | | || | || ||| | || || || || ||||||| | || | | || || | ||| | | | | || | || | | | | | | | | | || | || | | || ||| | ||||
gttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTT---TGAAAGTCATGGCGGAGCATTTGGCT--TCAATATTTGGGACTG-AGAAGGATAGGGTTAACTGCCCCTT-TTACTTCAAG
upper sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
--------------------ttgctaaatatcttgttcaatgactgatttcttaaactcagggtggaaattctgccat---ggcggagcatttggcttcaatctt--tggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT-
|| | | ||| |||| || || | | || | || ||| | || || || || |||||| || || | | || || | ||| | | | | || | || | | | | | | | | | || | || | | || ||| | ||||
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTT---TGAAAGTCATGGCGGAGCATTTGGCT--TCAATATTTGGGACTG-AGAAGGATAGGGTTAACTGCCCCTT-TTACTTCAAG
upper sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G031827_T02 (Zea mays), 3'ss of exon 1
----------------------------------------------------------ttgctaaatatcttgttcaatgactgatttcttaaac---tcagggtggaaattctgccatggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT
||| | || | ||| | || || | || |||| || || || |||||||||||| |||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||||||||| ||||| ||||
atccccatggttcttgataacaggccatgagtttataccccctccatttcaccttatattgaagatgatactattc--ttgcttatgcttgaaggttgtcagTCTGCAAGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGCTTGTCGTC-----------------------------------------------------------
upper sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G031827_T06 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------ttgctaaatatcttgttcaatgactgatttcttaaact---cagggtggaaattctgccatggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT
||| | || | ||| | || || | || | ||| || || || |||||||||||| |||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||||||||| ||
gtattccttgatccccatggttcttgataacaggccatgagtttataccccctccatttcaccttatattgaagatgatactattc--ttgcttatgcttgaagGTTGTCAGTCTGCAAGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC-------------------------------------------------------------------
upper sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G031827_T05 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------ttgctaaatatcttgttcaatgactgatttcttaaa---ctcagggtggaaattctgccatggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT
||| | || | ||| | || || | || |||| || || || |||||||||||| |||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||||||||| ||
attccttgatccccatggttcttgataacaggccatgagtttataccccctccatttcaccttatattgaagatgatactattc--ttgcttatgcttgaagGTTGTCAGTCTGCAAGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC-------------------------------------------------------------------
upper sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G020928_T03 (Zea mays), 3'ss of exon 2
--------------------------------------------------------ttgctaaatatcttgttcaatg--actgatttcttaaactcagggtggaaattctgc---------catggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT
| | || || | || || | | | | | | | ||| | ||||| |||||||||||| |||||||| ||||| || |||||||| ||||| || || |||||||| |||||||||||||| ||
catggttctagataacaaaccatgagtttatatcattatcccctctatctcaccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC-------------------------------------------------------------------
upper sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G020928_T02 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------ttgctaaatatcttgttcaatg--actgatttcttaaactcagggtggaaattctgc---------catggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT
| | || || | || || | | | | | | | ||| | ||||| |||||||||||| |||||||| ||||| || |||||||| ||||| || || |||||||| |||||||||||||| ||
gtattccttgatccccatggttctagataacaaaccatgagtttatatcattatcccctctatctcaccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC-------------------------------------------------------------------
upper sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G025014_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------ttgctaaatatcttgttcaatgac-tgatttcttaaactcaggg----------tggaaattctgccatggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT
| | || || | || || | || || || | || | || |||||||||||| |||||||| ||||| || |||||||| ||||| || || |||||||| |||||||||||||| ||
catggttctagataacaaaccatgagtttacatcattatcccctctatctcaccttatattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGAGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC-------------------------------------------------------------------Mapped 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|86038108|gb|DR333863.1|DR333863EST: AAATCCTTATGTCAGGAGATCCCATTCTCT AGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCG
genomic: AAATCCTTATGTCAGGAGATCCCATTCTCTgtctctctgt ... agaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaattctgccatggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT
aatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgctaaatatcttgttcaatgactgatttcttaaactcagggtggaaattctgccatggcggagcatttggcttcaatctttggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT
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