Sequence
atgc intronic sequence ATGC exonic sequence...tgactcttgatctggttggggccaaaatttaggataatagagtatttggctttttgtttctatgcgttgtgtagttagcttttttgttgtttgtcaacagGAGAAGAATCGGATCAACAAGGATGGTGAACTTGTGATATCTTCTACCAAAACCAGAACGCAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G62850.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g14510.2 (Oryza sativa), 3'ss of exon 3
tgactcttgatctggttggggccaaaatttaggataatagagtatttggctttttgtttctatgcgttgtgtagttagcttttttgt---tgtttgtca---acagGAGAAGAATCGGATCAACAAGGATGGTGAACTTGTGATATCTTCTACCAAAACCAGAACGCAGAA
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--------------gtataaaaaaaatcttcctcttttgcaaatcttcattgtcattttttctgtattgtctcaagaggttgtttatatttgcttggtatacacagGAAAAGAACCGGATAAATAAAGATGGGGAGCTTGTGATATCTTCTACAAAAACTAGGACACAAAA
upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G170532_T01 (Zea mays), 3'ss of exon 3
tgactcttgatctggttggggccaaaatttaggataatagagtatttggctttttgtttctatgcgttgtgtagttagcttttttgttgttt--gtcaacagGAGAAGAATCGGATCAACAAGGATGGTGAACTTGTGATATCTTCTACCAAAACCAGAACGCAGAA
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aatcatctagtcttatatgtatttttattaattcctttcatatatct--tttcttaatcatgtgaacagattgtttacattttgccttctctatgtgcacagGAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA
upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G03930.1 (Glycine max), 3'ss of exon 3
-tgactcttgatctggttggggccaaaatttaggataatagagtatttggctttttgtttctatgcgttgtgtagttagctt-ttttgttgtttgtcaacagGAGAAGAATCGGATCAACAAGGATGGTGAACTTGTGATATCTTCTACCAAAACCAGAACGCAGAA
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tttaatctcgacct--ttgttggtttattcctggtttgaatgatcatctacttacatctaccatacgttctattgatatttgattttgttggtgctgagcagGAGAAAAACCGTATTAACAAGGATGGGGAGCTTGTGATTTCTTCAACCAAAACTAGAACGCAGAA
upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G14410.1 (Glycine max), 3'ss of exon 3
tgactcttgatctggttggggccaaaatttaggataatagagtatttggctttttgtttcta---tgcgttgtgtagttagctt-ttttgttgtttgtcaacagGAGAAGAATCGGATCAACAAGGATGGTGAACTTGTGATATCTTCTACCAAAACCAGAACGCAGAA
||| | | | | || | || | | | || || | | || |||| | ||| | | | || | |||||||| | | | |||||||| || || || ||||||||||| || |||||||| ||||| ||||| || |||||||||||
---atctcaacc-gttgttggtttattcttggtttgaatgatcatctacttacttacgtctaccttatgttttattgatatttgattttgttgctgctgagcagGAGAAAAACCGTATTAACAAGGATGGGGAGCTTGTGATTTCTTCAACCAAGACTAGAACGCAGAA
upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0241g00090.t01 (Vitis vinifera), 3'ss of exon 4
-tgactcttgatctggttggggccaaaatttaggat--aatagagtat-ttggctttttgtttctatgcgttgtgtagttagcttttttgttgtttgtcaacagGAGAAGAATCGGATCAACAAGGATGGTGAACTTGTGATATCTTCTACCAAAACCAGAACGCAGAA
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ttattttttgtttttactattttatttatataaaattgggtctcgtttattgcctacttatctttctatga-gctttgttgactttcctagt---tatgaacagGAAAAGAATCGGATTAACAAAGATGGGGAGATTGTGATTTCTTCAACAAAAACTAGAACACAGAAMapped 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|125171148|gb|EL194200.1|EL194200EST: AACGTCGTATTGGCTGAGTGACAGGATCAGAGAGAAAATCTTACTGACG GAGAAGAATCGGATCAACAAGGAATGGTGAACTTGTGATATCTTCTACCAA
genomic: AACG-CGTATTGGCTGAGTGACAGGATCAGAGAGAAAATCTTACTGACGgtttgttttt ... ttgtcaacagGAGAAGAATCGGATCAACAAGGA-TGGTGAACTTGTGATATCTTCTACCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggctttttgtttctatgcgttgtgtagttagcttttttgttgtttgtcaacagGAGAAGAATCGGATCAACAAGGATGGTGAACTTGTGATATCTTCTACCAAAACCAGAACGCAGAA
cttttttgttgttt CT-rich tract
tttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgactcttgatctggttggggccaaaatttaggataatagagtatttggctttttgtttctatgcgttgtgtagttagcttttttgttgtttgtcaacagGAGAAGAATCGGATCAACAAGGATGGTGAACTTGTGATATCTTCTACCAAAACCAGAACGCAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG