Sequence
atgc intronic sequence ATGC exonic sequencegttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgtttctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggttttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G05780.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G05780.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 3
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgtttctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggttttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG---------
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-------------------------------------------------------------------------------taaagttaa---ttatgctagcttcgtcactgggtgctcctgctgtattgcctgtggcgct--tctcacagctgtttattccaattctcgctctccaaattgcagTTATGTTCCTAATCCAGTCTTGGTGATTATTGATGTCCAACCCAAGGAGCTGGGTATACCGACCAAAGCGTACTACGCTGTGGAGGAGGTTAAAGAG
upper sequence: AT5G05780.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 3
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgtttctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggtt-ttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG--------
||| ||| || | | | | || || | ||||| ||| || | | |||| | | | || | |||| | ||||||||||||||||||||| ||| |||| || |||||||| | ||||| ||| | |||||||| || |||||||| ||||| || || |||
--------------------------------------------------------------------------------tcttattctctttgcctctttatgtctttaacattttcatctgtagttttgtgtacct---gatcaatcttta-tccatattaatcaagcttaaaactgttgcaGCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA
upper sequence: AT5G05780.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 3
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgtttctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggtt-ttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG---------
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---------------------------------------------------------------------------------cttattctctttgcctctttctatctttatcatcttcatctgtagttttgtgtacct---gatcaatctttatccaaa-ttgatcaagcttaaaactatcgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG
upper sequence: AT5G05780.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G03160.1 (Glycine max), 3'ss of exon 2
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgttt--ctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggtt-ttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG---------
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-----------------------------------------------------------------------------------cttattctctttgcctctttctatctttaatgttttcatttgtagttttgtgtacct---gatcaatctttatccaaa-ttaatcaagcttaaaattgttgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTAGGAATCCCAAGAAAAACATATTATGTCGTTGAAGAGGTTAAAGAG
upper sequence: AT5G05780.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 3
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctg--aaatctgtgtttctttcccactttacgttttttgtggcttcggtttcatc--tccaattaaggttcactttgcttttggttttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG---------
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-------------------------------------------------------------------------------------gtgatcttggatcatcaaatatattgacatttctaacaatggaaattgattttccttcatctggtcggtgtgattaa---tcagtttctctttggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG
upper sequence: AT5G05780.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgtttctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggttttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG---------
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gtaagt--ccaatt---ttattctgaactctgcatgtcgtactatgtagatgtacgacgtggccgtaactacttcatgtatagtagt--tcttagaatgaatagaacttatacttggcaatatttgctacccctt-caagagtcttactcttaaccgaagtttttcatattcctt-tgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGMapped 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|124943617|gb|EL019786.1|EL019786EST: GGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGG CTATGTTCCAAATCCAGTCCTGGTCATTATTGA
genomic: GGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGGgttagtttcc ... ggttttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGA
EST:
gi|125308896|gb|EL322981.1|EL322981EST: AGAATGATTTGGATGTTCACGCGTTGTTCAATGG CTATGTTCCAAATCCAGTCCTGGTCATTATTGAATGTCCAGCCTAAAGAAC
genomic: AGAATGATTTGGATGTTCACGCGTTGTTCAATGGgttagtttcc ... ggttttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGA-TGTCCAGCCTAAAGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtggcttcggtttcatctccaattaaggttcactttgcttttggttttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG
aattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgtttctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggttttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG
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