Sequence
atgc intronic sequence ATGC exonic sequence...gtgccatttttgtccatagagtagtgaagatgccaatgtgatacagttgatctatcttatggttggtttcagttacagaatttagtctttttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG
Basic information
species | Glycine max |
transcript | GLYMA12G09560.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G09560.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g05900.1 (Oryza sativa), 3'ss of exon 4
gtgccatttttgtccatagagtagtgaagatgccaatgtgatacagttgatctatcttatggttggtttcagttacagaatttagtctttttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG
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---------------gtagtgt-gttatcctattgcgatcatggtactgatatttcattaggtggattctaactgttg---tcacacatgtaa--tgcagATGGCAGATCCCTTGACTGCATTGATGTATGCAGTACAAGTGATGAATTTTCTTAAGATGCTAATACAAAAAACCCTCAAGGATAGAGAAGAGTCTGATC
upper sequence: GLYMA12G09560.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
gtgccat-ttttgtccata---gagtagtgaagatgccaatgtgatacagttgatct--atcttatggttggtttcagttacagaat-ttagtctttttg-gttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG
|| || || ||| || | | | | | | ||| | | | | | | | |||| | | | | |||| || ||||||||||||| |||||||||||| ||||||||||||| ||||||||||| || || |||| || || || |||||| || ||| || | |
gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
upper sequence: GLYMA12G09560.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G113073_T01 (Zea mays), 3'ss of exon 4
gtgccat-ttttgtccatagagtagtg---aagatgccaatgtgatacagttgatctatcttatggttggtttcagttacagaatttagtctttttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG
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gtattgcattgtgctgatacgatagcgattagcaaactatcaatatatacttcacccatcacaa---tgatgctaactatagca------cgcttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCGACCC
upper sequence: GLYMA12G09560.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0080g00580.t01 (Vitis vinifera), 3'ss of exon 4
gtgccatttt----tgtccatagagtagtgaagatgccaatgtgatacagttgatcta-tcttatggttggtttcagttacagaatttagtctttttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG
|||||| | || || | | | | || | || | || || | | | | ||||| ||| | || | || | | |||||||||| ||| ||||||||||||||||||| || ||||| ||||| ||||| |||| ||||| ||| ||| || ||||||||| | ||| | |
---gcattttaagatttcaatcaataatttatcattttatcgttctgcaactgtttcaataacaccattggtaacagccttctatgtt--ttcttctcatcatagATGGCAGATCCTCTGACTGCATTGATGTATGCTGTCCAAGTCATGAATTTCCTCAAGACACTTATCATAAAGACACTACGAGAAAGAGAAGATTCAATGG
upper sequence: GLYMA12G09560.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
--gtgccatttttg-----tccatagagtagtga-----agatgccaat-gtgat---------acagttgatct-atctta------tggttggtttcagttacagaatttagtctttttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG-
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gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAG-GCGATAT
upper sequence: GLYMA12G09560.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S256_73V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------gtgccatttttgtccatagag--tagtgaagatgccaatgtgatacagttgatctatcttatggttggtttcagttacagaatttagtctttttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG-
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gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAG-GCGATACMapped 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|26058065|gb|CA800979.1|CA800979EST: AGATGAATGCACGGAACATCGCCATGGTTTTTGCACCAAATATGACTCAT ATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTC
genomic: AGATGAATGCACGGAACATCGCCATGGTTTTTGCACCAAATATGACTCATgtgagttcca ... ttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgatctatcttatggttggtttcagttacagaatttagtctttttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG
agttgat putative branch site (score: 5)
tcttttt putative PPT
aatttagtcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgccatttttgtccatagagtagtgaagatgccaatgtgatacagttgatctatcttatggttggtttcagttacagaatttagtctttttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
-tgccatt
- - - - - - - - - - - - - - gatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgg