Sequence
atgc intronic sequence ATGC exonic sequencegtgagtagtatatttctgtgtgttagccagtccagtccattagtttttttatttctcatttttttttttatcttggggttggtttaatttatagGACTTTTGGATGCTGGACGTGAAAACTAACCAATGGGAGCAGTTGAATTTGAAGGGATGTCCTAGTCCACGTTCTGGTCATCGTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50310.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 5
--gtgagtagtatatttctg--tgtgtta---gccagtccagtccattagtttttttatttctcatttttttttttatcttggggttggtttaatttatagGACTTTTGGATGCTGGACGTGAAAACTAACCAATGGGAGCAGTTGAATTTGAAGGGATGTCCTAGTCCACGTTCTGGTCATCGTATG
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gtttagctcacattctcttgcttttgttatgtgacgagaatgtggtttggtgtattggattttgactatttggtgatgtttatggatttttatttgtttagGATTTTTGGATGTTGGACCTGAAAACAAATCAGTGGGAGCAGCTTAATTTGAAAGGGTGCCCCAGTCCACGTTCAGGACATCGAATG
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 5
-------------------gtgagtagtatatttctgtgtgttagc----cagtccagtccattagtttttttatttctcatttttttttttatcttggggttggtttaatttatagGACTTTTGGATGCTGGACGTGAAAACTAACCAATGGGAGCAGTTGAATTTGAAGGGATGTCCTAGTCCACGTTCTGGTCATCGTATG
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gttaagctcacattgccttgcttttgatatgcgacgagattacaagaatgtggtttggtgtattggattttgactatttggttatgttattt--tttggattttgatttgttta--gGATTTTTGGATGTTGGACCTGAAAACAAATCAGTGGGAGCAGCTTAATTTGAAAGGGTGCCCCAGTCCACGTTCAGGACATCGAATG
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------gtgagtagtatatttctgtgtgttagccagtccagtcc-attagtttttttatttctcatttttttttttatcttggggt------tggtttaat-ttatagGACTTTTGGATGCTGGACGTGAAAACTAACCAATGGGAGCAGTTGAATTTGAAGGGATGTCCTAGTCCACGTTCTGGTCATCGTATG
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gtacgacacttgccatgtttcttcttattttgaagaaaacaatgtagtttattgttcattggagtcttggttgtgtttctataatttgtggtcaaggttagaacaatgcatttgctattttgctgttgcagGACTTTTGGGTGTTGGACCTGAAAACAAATCAATGGGAACAACTAAATCTGAAAGGATGTCCAAGTCCACGGTCAGGTCATCGAATGMapped 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|124732645|gb|EH824047.1|EH824047EST: CTCCGAATCAAGAGCGTTTCCATCACTACAAG GACTTTTGGATGCTGGACGTGAAAACTAACCAATGGGAGCAGTTGAATTTG
genomic: CTCCGAATCAAGAGCGTTTCCATCACTACAAGgtgagtagta ... taatttatagGACTTTTGGATGCTGGACGTGAAAACTAACCAATGGGAGCAGTTGAATTTG
EST:
gi|164060945|gb|ES063156.1|ES063156EST: GTGGTGAATTTACATCTCCGAATCAAGAGCGTTTCCATCACTACAAG GACTTTTGGATGCTGGACGTGAAAACTAACC
genomic: GTGGTGAATTTACATCTCCGAATCAAGAGCGTTTCCATCACTACAAGgtgagtagta ... taatttatagGACTTTTGGATGCTGGACGTGAAAACTAACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtttttttatttctcatttttttttttatcttggggttggtttaatttatagGACTTTTGGATGCTGGACGTGAAAACTAACCAATGGGAGCAGTTGAATTTGAAGGGATGTCCTAGTCCACGTTCTGGTCATCGTATG
gtttaat putative branch site (score: 4)
ttttttatttctcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtagtatatttctgtgtgttagccagtccagtccattagtttttttatttctcatttttttttttatcttggggttggtttaatttatagGACTTTTGGATGCTGGACGTGAAAACTAACCAATGGGAGCAGTTGAATTTGAAGGGATGTCCTAGTCCACGTTCTGGTCATCGTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG