Sequence
atgc intronic sequence ATGC exonic sequencegtaaacagagtcacttgttcatttttaaaaccttaaattttactgctgcctcataatgattaattttttatactccagagtcctgatatatatctatcacttacattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
Basic information
species | Glycine max |
transcript | GLYMA09G24970.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 6
gtaaacagagtcacttgttcatttttaaaaccttaaattttactgctgcctcataatgattaattttttatactccagagtcctgatata--tatctatcacttacattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
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---------------------gtagcaatttctttggttttctctct-tttctt--tggtttgtttgtatcggt--ggaattatggtgtaattataagtcctgttcatcacaatttt---gcagGGATATTAAAGGTGCAAATATACTAGTAGATCCTAGTGGTCGTGTTAAGCTTGCAGATTTTGGAATGGCAAAACAT
upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 6
gtaaacagagtcacttgttcatttttaaaaccttaaattttactgctgcctcataatgattaattttttatactccagagtcctgat-atatatctatcacttacattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
|| || | | ||||| | || ||| | | || | | | | | | | ||| | ||| || | ||| | | || ||| ||| | ||||||| ||||| ||||| |||||||||||| ||||||| || || ||| | || ||||| || |||||||| |||
---------gtaacat-tccatttc-----cttttgtcgttagttcagcacttcagttccttagatgtaagctaccaagttgtagattattttattatttgtcatgttccataatttgca--gGGACATTAAAGGTGCAAACATACTGGTAGATCCTAATGGTCGTGTAAAGCTTGCTGACTTCGGAATGGCAAAACAT
upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 6
gtaaacagagtcacttgttcatttttaaaaccttaaattttactgctgcctcataatgattaattttttatactccagagtcctgatatat-atctatcacttacattgcatttcttgtaaa------gGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
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------------------------gtaacataatttttttagattcccttttccggtctattattttatgcatactaggggtttgctattttatcttttcttttgcttactctcttcctaaatttgcagAGACATCAAAGGTGCAAACATATTGGTAGACCCTAATGGCCGTGTAAAGCTTGCTGACTTTGGGATGGCAAAACAT
upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 5
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 5
gtaaacagagtcacttg--ttcatttttaaaaccttaaattttactgctgcctcataatgattaattttttatactccagagtcctgatatatatctatcacttacattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
|||| | | | || |||| | ||| |||||| ||| | || | | | ||| || | || | || || | || ||| | || ||||||||||| ||||| ||| ||||||| |||||||||| || ||| | || |||||||| |||||||| |||
gtaacataatttgtatagttttccttttccagcctattatttta----tgcttactagaggtctgctatttttatttttttttcttt-tacttactctcttcctaaatt----------tgcagAGACATCAAAGGCGCAAACATATTGGTAGACCCTAATGGCCGCGTGAAGCTCGCTGACTTTGGGATGGCAAAACAT
upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 5
gtaaacagagtcacttgttcatttttaaaaccttaaattttactgctgcctcataatgattaattttttatactccagagtcctgatatatatctatcacttacattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
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----gtagaat------ttcattttttttgggttcaatcttttgggttgcacatt-cagcaaatgacatctatttttgcttttgcttttgtgtgtgctatcaata----atttgt-----agGGACATCAAAGGTGCCAACATACTAGTAAATCCAAGTGGCCGTGTTAAGCTTGCAGACTTTGGAATGGCAAAACAT
upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 5
gtaaacagagtcacttgttcat--ttttaaaaccttaaattttactgctgcctcataatgatta----attttttatactccagagtcctgatatatatctatcacttacattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
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gtgaatcaagttaccaattgttgatccaacaatctgaagtgtagctgctttttattgatttttctattatttgctttatttca-aactttgttcaccttttttctcacaaaccatatttcctgtacagGGATATTAAAGGGGCAAATATACTTGTAGACCCAAGTGGTCGAGTCAAGTTAGCAGATTTTGGAATGGCAAAGCATMapped 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|5753494|gb|AI960781.1|AI960781EST: CAAATTTTGTCAGGACTTGCTTATTTACATGCTAAAAATACTGTCCACAG GGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTT
genomic: CAAATTTTGTCAGGACTTGCTTATTTACATGCTAAAAATACTGTCCACAGgtaaacagag ... tcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatactccagagtcctgatatatatctatcacttacattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
cacttac putative branch site (score: 2)
catttctt putative PPT
tgatatatatctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacagagtcacttgttcatttttaaaaccttaaattttactgctgcctcataatgattaattttttatactccagagtcctgatatatatctatcacttacattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG