Sequence
atgc intronic sequence ATGC exonic sequence...gtcctttgatacacttgccgtgaactactaacatctgtttttcctttttcctgtatttcactggtgttttctgatatcctttttaatgtgtttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCCATGGCTTCTTCCTTTGGGCTGCATGGCCA
Basic information
species | Glycine max |
transcript | GLYMA18G08230.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 7
----gtcctttgatacacttgccgtgaactactaacatctgtttttccttt-ttcctgtatttcactggtgttttctgatatcctttttaatgtgtttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCCATGGCTTCTTCCTTTGGGCTGCATGGCCA----
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gatttagtctggatactttttttcttcctattttacttcgattgctctttggttactccatttcacagacctaagtacctaaccatatcaac----tttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAA-----TCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT
upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
---------------------------------------------------------------------------------------gtcct-ttgatacacttgccgtgaact---actaacatctgtttttcctttttcctgtatttcactggtgt---tttctgatatcctttttaatgtgtttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCCATGGCT-TCTTCCTTTGGGCTGCATGGCCA
| | | |||| ||| | | | | | | | || | || | | || |||| | ||| || | | | | |||| |||||||||||||||| ||||| ||||||||||| || ||||| || || || ||||| |||| | | ||| | || ||| |||| ||
gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagttctacttcaaccaaatcaatttatggttctaatcatgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGGACTGCTTGCT--
upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
gtcctttgatacacttgccgtgaactactaacatct---gtttttcctttttcctgtatttcactggtgttttctgatatccttt--ttaatgtgtttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGATACTTGAAGATAATT--TCTCCCATGGCTTCTTCCTTTGGGCTGCATGGCCA
|| ||| | | | ||| | || || | | | | | ||| ||| || ||| | ||| | | || || | | ||||| ||||||||||||||| ||||| || |||||||| ||||| || || || || |||| |||| | || | | || | || | ||
---ctgtgagaggcaacgcatgatatgctgtcagttcaaagtatagatgactattgtctttt-cttgtgatatctcacaagtttgcattgctatatttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGATATTC---
upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 7
---gtcctttgatacacttgc---cgtgaactactaacatctgtttttcctttttcctgt-atttcactggtgttttctgatatcctttttaatgtgtttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCCATGGCTTCTTCCTTTGGGCTGCATGGCCA-
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cttttatcattgtacacttatggacaaaaaatgcaattggatgctatgagcttctcaaaccactcaactgatgttg------atttgttttatttcctttgaacagGGACATCACCACCACATTCCCAAGCTTTGTCTTTCATTCTCAAGTTGACGACACCTGAAG-TCCCATACATGAAAGTTGACTGGTTTTTGTTA-ATAATTGCMapped 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|151397479|gb|EV267352.1|EV267352EST: TTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCTTCAATACCTCAAG GACATCACCACAACATTCCCGAGCTTTGTATTTCATT
genomic: TTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCTTCAATACCTCAAGtaattcttta ... tttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATT
EST:
gi|13791269|gb|BG653860.1|BG653860EST: TTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCTTCAATACCTCAAG GACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGAT
genomic: TTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCTTCAATACCTCAAGtaattcttta ... tttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcctgtatttcactggtgttttctgatatcctttttaatgtgtttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCCATGGCTTCTTCCTTTGGGCTGCATGGCCA
ttttaat putative branch site (score: 3)
atatcctttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcctttgatacacttgccgtgaactactaacatctgtttttcctttttcctgtatttcactggtgttttctgatatcctttttaatgtgtttgggcaggGACATCACCACAACATTCCCGAGCTTTGTATTTCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCCATGGCTTCTTCCTTTGGGCTGCATGGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
-tcctttg
- - - - - -cacttgc
- - - - - - - - - cgtgaac
- - - - - - - - - - - - - actaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgttt