Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttgtctttttctttcatgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatctatgttctttgatatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
Basic information
species | Glycine max |
transcript | GLYMA07G14870.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 8
gtaagtttgtctttttctttcatgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatctatgttctttgatatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
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----------------------------gtaagtgcaattttctgtgcttcatcccttttgaggaagttccgtcaactaatggtgaa--gactaaaatctataattttt-----attgaaagGTGAGCCTTGTGCAAATTCCTGGCAAAGAGGAGCTGCGGCAGAAAAACCTTTTCAGTGTCAGTGATTGCAAGATGTACTGGCAGAACAGTGGAGAATATC
upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 8
gtaagtttgtctttttctttcatgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatctatgttctttgatatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
|| | | ||||| || || || ||| | || | || || || | | | || ||||| | | || | |||| ||||| | |||||||| |||||||||| || | ||||| |||||||||||||||||||| || ||||| || ||||||| || |||||| || |
----------------------------gtgagcataaatttgtggaacagatacctcttataccatgtttattcaataactaatgataaaggctaaaat-tgatcttt--tctgttgaaagGTGAGTCTAGTGCAAATCCCTGGCAAAGAGGAGCTGCGACAGAAAAACCTTTTCAGTGTCAGTGATTGTAAGATGTATTGGCAAAACAGTGGAGAATATC
upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtttgtctttttctttcatgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatctatgttctttgatata----tttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
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gtatgttt-cttttatttcttatgtaaatga---aaagccctg----------atacctcaataatcttccgt---ttctctgccagttgttttgtatttacatg--ttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtttgtctttttctttcatgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatctatgttctttgatatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
||| |||| | || || | | ||||||||| |||| | || | | | | | | || | | | ||| ||||| || | || | | || | ||||| || | |||||||| ||||| | ||| || ||||||||||| || |||||||| || ||||||||||| |||||||| || | |||||| || |
gtatgtttctattatt-tctgatgtacatga---aaagctctgaat--ccttaatttgcttctgtttctctgcctggtgttttgaaattac---atgttgatatccctt-------cttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S138_36V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagttt--gtctttttcttt---catgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatcta-----------------------tgttc----tttgatatatttat-agGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
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gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatccttcagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT
upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S130_248V6.2 (Physcomitrella patens), 3'ss of exon 6
-----------------gtaagtttgtctttttctttcatgtacatg-gattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatat------ctatgttctttgatatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
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gtgagtttttaccccctttctatttgatattttgtttcatacttgggtaatccggaacttttttgaggacgatagcatattgtttgacctcctgc-atgaaggcaatactgaaaataatggacaatgatttgtggtatcttt-cagGTGAGTCTTGTGTCTATTCCCAGCAGAGAAGAGTTGCGTCAAAAGAACCTTTTCAGCGTGAGTGACTGCAAAATGTATTGGCAAAGCAACGGTGAGTACT
upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ13839 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtttgtctttttctttcatgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatctatgttctttgatatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
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-------------------------------------------------------------gtatgtatttgtgtttgatttctc---tacatgtgacctggtttgctcttgacttcaacagGTTAGCCTGGTTCAAATTCCTGGCAGGGAAGAACTGAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAACGGAGACTATC
upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ12681 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtttgtctttttctttcatgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatctatgttctttgatatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
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-------------------------------------------------------------gtatgtatttgtgtttgatttctc---tacatgtgacctggtttgctctcaacttcaacagGTCAGCCTGGTTCAAATTCCTGGCAGGGAAGAACTGAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAACGGAGACTATCMapped 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|254330176|gb|GR839729.1|GR839729EST: TTATTGCTCTTTTTGTTCCTGAGATGGGAGGCGGTAACCAGCCTGCCAGG GTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTT
genomic: TTATTGCTCTTTTTGTTCCTGAGATGGGAGGCGGTAACCAGCCTGCCAGGgtaagtttgt ... atatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTT
EST:
gi|192294005|gb|FG987174.1|FG987174EST: TTATTGCTCTTTTTGTTCCTGAGATGGGAGGCGGTAACCAGCCTGCCAGG GTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTT
genomic: TTATTGCTCTTTTTGTTCCTGAGATGGGAGGCGGTAACCAGCCTGCCAGGgtaagtttgt ... atatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtcatatattatttatcaattattttatatctatgttctttgatatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
ctttgat putative branch site (score: 5)
tatattatttatcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttgtctttttctttcatgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatctatgttctttgatatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA