Sequence
atgc intronic sequence ATGC exonic sequencegtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGACATGGAAAGTTTCAAGGAGTTTTTCGAGAGCCCATCTTTTAGAGCAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50320.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 3'ss of exon 4
gtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGACATGGAAAGTTTCAAGGAGTTTTTCGAGAGCCCATCTTTTAGAGCAGATG
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----------------------------------gtagtctccttaaatcattaatcatctcgtttagtcaactt-----------gttgctggc----agcatttgttaaaataaagtatcatctcatatggttga---actgttttaat----------cctccattgattacctt-ttgatagGTGGTCGCCCACATGATGCCAGATTTACCTAATGTTGGAGTTGAAAGAGATCTGGAAAGTTTCCGAGAATTTTTTGAAAATCCAGCATTCCGAGCTGATG
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 4
gtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttatt-ttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGACATGGAAAGTTTCAAGGAGTTTTTCGAGAGCCCATCTTTTAGAGCAGATG
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---------------------------------------------------------------------------------------------gttattgtttttttt--agtcacataactttgtctgattgctttcattgtttgtttatgattattctagttgttttgattcacccttttgacagGTGGTTGCCCACATGATGCCAGATTTACCTAATGTTGGAGTTGAAAGAGACTTAGAAAGTTTCAGAGAGTTTTTTGAAAGTCCAGCATTCCGGGCTGATG
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G359735_T03 (Zea mays), 3'ss of exon 4
gtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaa-tatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGACATGGAAAGTTTCAAGGAGTTTTTCGAGAGCCCATCTTTTAGAGCAGATG
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--------------------------------------------------------------------------------------gtttttttttgtcacctagctttgc--ttaattgattttattatttgtttatgattgttctga----------ctatcttgattcacccttttg---acagGTGGTTGCCCACATGATGCCAGATTTACCTAATGTTGGAGTTGAAAGAGATTTGGAAAGTTTCAGAGAATTTTTTGGAAGTCCAGCGTTCCGGGCTGATG
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G18150.1 (Glycine max), 3'ss of exon 4
gtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGACATGGAAAGTTTCAAGGAGTTTTTCGAGAGCCCATCTTTTAGAGCAGATG
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---------------------------------------------------------------------------------aatatggactaggttagtaatgtccc---atctcatgaatgttatcccactt--gctctttcttttcatttagtttatgcttattattttgggcttttgctttagGTTGTTGCTCATATGATGCCTGATCTTCCAAATGTTGGTGTTGAAAGGGACATGGAAAGTTTCCGGGAGTTTTTTGAGAGTCCCTTGTTTAGAGCAGATG
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G36790.1 (Glycine max), 3'ss of exon 4
gtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttc--attttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGACATGGAAAGTTTCAAGGAGTTTTTCGAGAGCCCATCTTTTAGAGCAGATG
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--------------------------------------------------------------------------------gaatatggactaggttagta----cgtctcatcttatgaatgttatcccactttc----tctttcttctcatgtagtttttgcttaatttttttggcttttgctttagGTTGTTGCTCACATGATGCCTGACCTTCCTAATGTTGGTGTTGAAAGGGACATGGAAAGTTTCCGGGAGTTTTTTGAGAGCCCCATGTTTAGAGCAGATG
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 3'ss of exon 4
gtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgttttt-cattttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGACATGGAAAGTTTCAAGGAGTTTTTCGAGAGCCCATCTTTTAGAGCAGATG
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-------------------------------------------------------------------------------ttaatttctttgcaatgattgg-atcctta----caacatgcatcagactaatcttg---caattttggagttttctacttgttgctaatttcatgcttttgctgtagGTTGTTGCTCATATGATGCCTGACCTTCCAAATGTTGGGGTAGAGAGGGACTTGGAAAGTTTCCGGGAGTTTTTTGAAAGCCCTATGTTTAGAGCTGATGMapped 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|125232764|gb|EL246849.1|EL246849EST: CTGGTTTCAAG GTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGAC
genomic: CTGGTTTCAAGgtattccctt ... ttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGACATGGAAAGTTTCAAGGAGTTTTTCGAGAGCCCATCTTTTAGAGCAGATG
tccttac putative branch site (score: 2)
tccttacctccgtttt CT-rich tract
taaatttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGACATGGAAAGTTTCAAGGAGTTTTTCGAGAGCCCATCTTTTAGAGCAGATG
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