Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacagctgaagcattaggatccatctatctgtcatacctattctctgactgtagcagctcaccatttgtttctggattctttgcagGACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03940.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 13
gtaaaacagctgaagcattaggatccatctatctgtcatacctattctctgactgtagcagctcaccatttgtttctggattctttgcagGACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAG
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---gtatggtctcgattctcatgcatagtgctttttctaagcaaggctacatttataagctacaagtgtcttttcttgcacttt----agGATTGGATTATGGAGCAGTGGGAAAATAACTACTACATCAGTGCCATAGCTGGTGCAATGAATGGGAGTTCCTTGGTGGTCATGTCAAAAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 13
-------------------------gtaaaacagctgaagcattaggatccatctatctgtcatacctattctctgac--tgtagcagctcaccatttgtttctggattctttgcagGACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAG
||| || || | | | | | ||| || | | | | ||| | | | | | | | ||| | ||||||||||| ||||| || ||||| || || |||||||||||||| |||||||| ||| ||||||||| || |||||||| ||| | ||||
gtgggttttttcttccttgatttatataattcatcttttgt-taaataaatacgtatgagttaaattaaataattgatgtcttggtgctgggctgctggcattttgatctct--cagGACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 13
-gtaaaacagctgaagcattaggatccatctatctgtcatacctattctc-----tgactgtagcagctcaccatttgtttctggattctttgcagGACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAG
|| | | | || || || ||||| | | || | ||| | || ||| || || |||||| | |||| ||||| |||||||| ||||||||||| ||||| ||||| || ||||| || || |||||| || || |||||||| ||| ||||||
gttattttttttcatgtgttgatttctat-tatcttctgtgagtgggttcatgcatacctgatactactgacctttcacttttggattttcactagGATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
---------gtaaaacagctgaagcattaggatccatctatctgtcatacctatt----ctctgactgtagcagctcaccatttgtttctggattctttgcagGACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAG
| | | | || | | | | | || | ||| | | || | | | | || | | | | | | ||||| |||||||||||||| ||||||||||| | |||||||||| | || ||||| || |||||||| ||||| ||||| || ||| | ||||
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------gtaaaacagctgaagcat-taggatccatctatctgtcatacctattctctgactgtagcagctcaccatttgtttctggat----tctttgcagGACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAG
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gtgggtgtgtggtgtctcgctcaagttttgggtagtatatgcagcttgtcgttcaatgatagaacagctatccctgttatgcgccatgccctcacattgagtcatatttttacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGMapped 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|125087162|gb|EL146386.1|EL146386EST: CTGGTTTCAGTTCTCAAGTTTATGAACTGTCCTCAGTCTTCCTGCACAAG GACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCC
genomic: CTGGTTTCAGTTCTCAAGTTTATGAACTGTCCTCAGTCTTCCTGCACAAGgtaaaacagc ... ttctttgcagGACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatacctattctctgactgtagcagctcaccatttgtttctggattctttgcagGACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAG
agctcac putative branch site (score: 3)
ttctttgc putative PPT
atttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacagctgaagcattaggatccatctatctgtcatacctattctctgactgtagcagctcaccatttgtttctggattctttgcagGACTGGATCATGGAACAATGGGAAAAGAACTACTATATCAGTTCCATAGCTGGTGCAAATAATGGAAGCTCGTTGGTTGTTATGGCTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG