Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaattcaaggataatgtatgcaactacaatctctgttttcttgcatattaaacaagaagcttatataaattaataattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
Basic information
species | Glycine max |
transcript | GLYMA05G35990.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g09550.3 (Oryza sativa), 3'ss of exon 2
gtaagtaattcaaggataatgtatgcaactacaatc-tctgttttcttgcat--attaaacaagaagc--ttatataaattaataat-tcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
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gtaagtcttgttgaaatcaattgtgtgtttgaaagcatgcagagtattacaataagtaaacttgcagccattggttgaatcaattgtgtgtttgggcatgcagAGCAAGATACGGCGTGCAGTTAGAAAAGGGTGCATTTGAAAAGCGCACAGCTGATTTCTTGTGGATGATGATATTTGGTGCCATATCACTGCTG
upper sequence: GLYMA05G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143817_T01 (Zea mays), 3'ss of exon 3
gtaagtaattcaaggataatgtatgcaactacaatc---tctgttttcttgcatattaaacaagaagcttatataaattaataattcttaaattct-----acagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
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----gtaagtgaaagtttttctgaacaccgatgataaaatatggttacttccacagtatatataattttaaatcaggttggggtttttgaaatttctttgcatagAGCAAGGTATGGTGTCATGTTGGAAAAGGGAGCATTTGATAAACGGACTGCAGATTTCTTGTGGATGATGATATTTGGTGCCATCTCACTATTG
upper sequence: GLYMA05G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G117388_T01 (Zea mays), 3'ss of exon 3
-------------------gtaagtaattcaaggataatgtatgcaactacaatctctgttttcttgcatattaaacaagaa-gcttatataaa-ttaataattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
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gtaggttaaagttttgctgactactgattataaaatagtg---acagttatgaactatctataattgtaaattagctttggttgtttggatttgctttatcgtgttttggca-tgcagAGCAAGGTATGGTGTCATGTTGGAAAAGGGTGCATTTGATAAGCGGACTGCAGATTTCTTATGGATGATGATATTTGGTGCCATCTCACTATTG
upper sequence: GLYMA05G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G29330.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtaattcaaggata-atgtatgcaactacaatctctgttttcttgcatattaaac-aagaagcttatataaattaataattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
|| || | | | || ||| | |||| ||| | ||||| || | || | ||||| ||| | ||||| ||| ||||| || ||||| |||||||| |||||||| | ||||| || || || |||||||||||||| ||||| |||| | ||||||
gtgagcatactattttcacatatatagatgaacaaagctaatttcgatttttattatcttaacatactcttttaaat------------gattgtgcagAGCAAGATATGGAGTTCAACTCGAGAAAGGGCCATTTGAAAGGCGGACAGCAGACTTTTTGTGGATGATGATCTTTGGATCCTTCACTCTATTG
upper sequence: GLYMA05G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g00510.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------gtaagtaattcaaggataatgtatgcaactacaatctctgttttcttgcatat-taaacaagaagcttatataaattaataattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
|||| | | | | | | | | || || || || | | | | | || | || | | | || | || | ||||||| || ||||| ||||| || ||||| ||| |||||| | || || || |||||||||||||||||||||||||| || | || | ||
gtaagtgtaactgtgtaaatcccagaagcttctcttgagttcaccctgaagtctgtgtgcacacttttgtggatttccatgtaacttgtctagagtttgtaggggaaccttgaaaaattgcttcatggaacctacctttaccctgcatttacatactgcaaagttatat-tgttacagAGCCAGATATGGGGTCCAGCTGGAGAAGGGAGTATTTGAAAGGCGCACGGCAGATTTCTTGTGGATGATGATATTTGGAGCTCTGACATTGCTGMapped 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|19346875|gb|BM891763.1|BM891763EST: TTTTTCCTTGGACCGTTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGC
genomic: TTTTTCCTTGGACCGTTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGC
EST:
gi|298164512|gb|HO014157.1|HO014157EST: TTTTTCCTTGGACCGTTCTCTATCAATTTTGGGATCCGTCTCCTAATGAT AGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGC
genomic: TTTTTCCTTGGACCGTTCTCTATCAATTTTGGGATCCGTCTCCTAATGATgtaagtaatt ... aattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgcatattaaacaagaagcttatataaattaataattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
aattaat putative branch site (score: 3)
atattaaacaagaagc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaattcaaggataatgtatgcaactacaatctctgttttcttgcatattaaacaagaagcttatataaattaataattcttaaattctacagAGTAAGGTATGGTGTCCAACTTGAGAAAGGACCATTTGACCGACGGACTGCTGATTTCTTGTGGATGATGATATTTGGTGCCTTTGCACTATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT