Sequence
atgc intronic sequence ATGC exonic sequencegtttaggattgttttttgtccatgttacttcaaacattgaataatacttaaacacaaacttcgtgaatctagtcacttcttcagtgacttacttatcacttaagggtttcagGTTTTTGAAGGAACATCTGGAATTGACAACAAGTTTACAACCGTGCAATTCACAGGAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G76030.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 4
gtttaggattgttttttgtccatgt---tacttcaaacattgaataatacttaaacacaaactt-cgtgaatctagtcac-ttcttcagtg-acttac---ttatcactta------agggtttcagGTTTTTGAAGGAACATCTGGAATTGACAACAAGTTTACAACCGTGCAATTCACAGGAGAG
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-gttatcatttttctatttttatgaatatcttttttgcttgagattgtattcagatttgcatttaccctatgatagttccattatccagagcacttacgttttattactgacttacttgattttcagGTCTTTGAAGGCACTTCAGGAATAGACAACAAATATACCACTGTGCAGTTCACAGGAGAG
upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 4
----gtttaggattgttttttgtccatgttacttcaaacattgaataatacttaaacacaaacttcgtgaatctag--tcacttcttcagtgacttacttatcacttaa--gggtt-----tcagGTTTTTGAAGGAACATCTGGAATTGACAACAAGTTTACAACCGTGCAATTCACAGGAGAG
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gttacttctccattgccttattgtcttttagtagtagttccaaattgatgttgattttacagtatggttaggctaggtctatttcctgaaaacttagtttgttaattaactgcattattcatcagGTTTTTGAAGGAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG
upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 4
-------------gtttaggattgttttttgtccatgttacttcaaacattgaataatacttaaacacaaacttcgtgaatctagtcacttcttcagtgacttacttatca-cttaagggtt--tcagGTTTTTGAAGGAACATCTGGAATTGACAACAAGTTTACAACCGTGCAATTCACAGGAGAG
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gttacttctccattctcctgattgttttttagcagtagttctaatttgattt--tgattctgcagtatggtcatgttagttccattcccagaaaacttagtttgttaattaactgcattattcatcagGTCTTTGAAGGAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG
upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 4
gtttaggattgttttttgtccatgttacttcaaacattgaataatacttaaacacaaacttcgtgaatctagtcacttcttcagtgacttacttatcacttaagggtttc-agGTTTTTGAAGGAACATCTGGAATTGACAACAAGTTTACAACCGTGCAATTCACAGGAGAG
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------------ctgctaccttttaagttttaatctttagatggtatatagtta-atagtatataatttctctcttattttagcttgatcattttctgttttaatttccccagGTTTTTGAAGGCACTTCTGGAATTGACAACAAATACACAACCGTGCAATTTACTGGGGAGMapped 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|125314115|gb|EL328200.1|EL328200EST: CGAGACGTGGTCAGGTTTTGGAAGTTGATGGCGAGAAAGCAGTTGTGCAG GTTTTTGAAGGAACATCTGGAATTG
genomic: CGAGACGTGGTCAGGTTTTGGAAGTTGATGGCGAGAAAGCAGTTGTGCAGgtttaggatt ... agggtttcagGTTTTTGAAGGAACATCTGGAATTG
EST:
gi|125091242|gb|EL149065.1|EL149065EST: TGGCGAGAAAGCAGTTGTGCAG GTTTTTGAAGGAACATCTGGAATTGACAACAAGTTTACAACCGTGCAATTC
genomic: TGGCGAGAAAGCAGTTGTGCAGgtttaggatt ... agggtttcagGTTTTTGAAGGAACATCTGGAATTGACAACAAGTTTACAACCGTGCAATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttcgtgaatctagtcacttcttcagtgacttacttatcacttaagggtttcagGTTTTTGAAGGAACATCTGGAATTGACAACAAGTTTACAACCGTGCAATTCACAGGAGAG
gacttac putative branch site (score: 2)
ttacttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaggattgttttttgtccatgttacttcaaacattgaataatacttaaacacaaacttcgtgaatctagtcacttcttcagtgacttacttatcacttaagggtttcagGTTTTTGAAGGAACATCTGGAATTGACAACAAGTTTACAACCGTGCAATTCACAGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA