Sequence
atgc intronic sequence ATGC exonic sequence...ttagcttttctttgtggttttaatggtagattttaggagtagtgtaaaatagagctctttgagcctatcataatttaaatattttgttgggccctgccagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
Basic information
species | Glycine max |
transcript | GLYMA19G17660.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G17660.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
ttagcttttctttgtggttttaat-ggtagattttaggagtagtgtaaaatagagctctttgagcctatcataatttaaatattttgttgggccctgccagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
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-gtgcttatacaagtttctctagtcaattggttttct---ttacatattctgcag-tcattactctaattattttgctcgtaacttctt----cctgt-agATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
upper sequence: GLYMA19G17660.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 5
ttagcttttctttgtggttttaatggtagattttaggagtagtgtaaaatagagctctttgagcctatcataatttaaatattttgttgggccctgccagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
|| | ||| |||| |||| | || | || || | | || ||| || || || || ||| ||||| ||||||||||| || ||||| || |||| |||||||| | ||||| || |||||||| || ||||||||||| || |||||| | || || ||||
----------------gtcct--tggatcatttctttcatagtctttgatgcaataaattt-gcttgt-attattaaattacattctta----ctggcagATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAAATACAAA
upper sequence: GLYMA19G17660.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 5
--------ttagcttttctttgtg-------gttttaatggtagatttt-aggag---tagtgtaaa-atagagctctttgagcctatcataatttaaatattttgttgggccctgc-cagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
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gtatttttttagccctgtttggtcagatgacgcattcctgctctgttctcatgtgcccttatatatatgtaaaacatttta---ttatggtaatctaaggatttt--tggacactgaacagATTTTGAAAGAACTTCACAAATCTTGTCGAAGAGAAGATGGTACAGATGATCAAAAGAAAGGAACCCAACTTTTGGAAGTATATGCAATTGAGATTCAAA
upper sequence: GLYMA19G17660.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 5
-----ttagcttttctttgtggttttaatggtagattttaggagtagtgtaaaatagagctctttgagcctatcataatttaaatattttgttgggccctgccagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
|| | | | ||| | | | || ||||| ||| || | | | | | | | || | | || | | | ||||||||||||| ||||||||||| |||||||| |||||||||||||||||||| ||||| || || || || |||| || ||||| | || ||||| |
actccttggtatacatcagtgttatgtagaataacttttat-agt--tgcactgcatcgtcagtagcatcatatgtgatgctgaccaatggtcgtgtgtt--tagATCTTGAAGGAGCTTCACAAATCTTGTCAAAAGGAAGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGA
upper sequence: GLYMA19G17660.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------ttagcttttctttgtggttttaatggtagattttagga------gtagtgtaaaatagagctctt----tgagccta-tcataatttaaatattttgttgggccctgccagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
| || || | | || ||| ||| | | ||| ||| | || | ||| |||| | | | || | | |||| | | ||||| |||||||| || || ||||| ||||| || |||||||| ||||||||||| ||||| || || ||| | ||||||| ||||| |||||||||| |
gtaagtattctgcccgttgactcctcaactttattttcatatctttcaactttatctagtattgaatgatttcgtttactcggaataccagtacttttcaaaatgggatgtaatgtgtagtaaattccttgttctgagaaaacttgtgatactcacagcttgtcgtacgt--gcagATTTTGAAGGAGCTCCATAAATCTTGTCAGAAGGAAGATGGTACAGATGACCAGAAGAAGGGCACACAATTGCTGGAGGTGTATGCGATAGAGATTCAGA
upper sequence: GLYMA19G17660.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------ttagcttttctttgtggttttaatggtagattttaggagtagtgtaaaatagagctctttgagc-ctatcataatttaaatatt-ttgttgggccctgccagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
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gtaagttcgctgccagttgatttctccacaatatcttcatatgtcctattttatctgataataaatgtcagtcgcttatctcaatgcttttcagttcgagatatatgttc---gcagaatatattttttcgtacacaaatgtgagatgcttctaatttcttagaactgc-agATTTTGAAGGAGCTCCACAAATCTTGTCAGAAAGAAGATGGTACAGATGATCAGAAGAAGGGCACACAATTGCTCGAGGTTTATGCGATAGAGATTCAGAMapped 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|15285921|gb|BI469812.1|BI469812EST: AGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGCATGAGTAAG ATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGAC
genomic: AGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGCATGAGTAAGgtgattttgc ... gccctgccagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatagagctctttgagcctatcataatttaaatattttgttgggccctgccagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
ccctgcc CT-rich tract
tatcataatttaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagcttttctttgtggttttaatggtagattttaggagtagtgtaaaatagagctctttgagcctatcataatttaaatattttgttgggccctgccagATCTTGAAGGAACTTCACAAATCCTGTCAAAAAGAAGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG