Sequence
atgc intronic sequence ATGC exonic sequence...gtatattctacgtggaaattttggggttatccaagataattgtgttatattacagcttttcttagtgtagaacagtgttaatgttcagctcttactgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
Basic information
species | Glycine max |
transcript | GLYMA13G28650.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47180.1 (Oryza sativa), 3'ss of exon 6
----gtatattctacgtggaaattttgg--ggttatccaag-ataattgtgttatattacagcttt--tcttagtg-tagaacagtgttaatgtt-cagctcttac------------tgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
|| || | | |||| | | | || || || | ||| | || | ||||||| |||||| | |||||| | |||||| | | | || || |||||||||||||| |||||||||||||| ||||| ||||| || || || ||||| || || || ||||||||||||| ||||
gtatgtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
upper sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
gtatattctacgtggaaattttgg--ggttatccaag-ataattgtgttatattacagctttt--cttagtg-tagaacagtgttaatgtt-cagctcttac------------tgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
|| || | | |||| | | | || || || | ||| | || | ||||||| |||||| | |||||| | |||||| | | | || || |||||||||||||| |||||||||||||| ||||| ||||| || || || ||||| || || || ||||||||||||| ||||
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
upper sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 5
gtatattctacgtggaaattttggggttatccaagataattgtgttatattacagct--tttcttagtgtagaacagtgttaatgttcagctct-tactgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC------
| | || | || | || | | | ||| | ||| | ||| | | | || | | | | | |||| | || | | | |||||||||||||| || ||||||||||| |||||||||||||| || || ||||| || | |||||| |||| ||
---ggtctcatttgatttactatggcccaaaatggagcccggcactctcttaatgtaaattttgcaatgtctctaatttgtcccatttatttatatcttacagAAAAGGAGATTAGTAACACATGCAAATGCAAAAAGCAAGAGTGAAAAGTTTCCTCCTCCGCATCAGGATGGTGCGGT------CTCTTTGGTTTCTACAAATCACA
upper sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 6
---gtatattctacgtggaaattttggggttatccaagataattgtgttatattacagcttttcttagtgtagaacagtgttaatgttcag-ctcttact----gcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
||| | | | ||| | || | | | | | | || ||| |||| | | ||| | || | | |||||| | |||||| || || |||| || ||||||||||| ||||| || |||||||||||||||||||| || || ||||||| | || |||| | || || |
gtgccatagcccataagtaaactc--aggctgtttg---tcactttcaaatgttattgcttaatatgatactgaatattgaggtttccaaatctcttattaacagCAGAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCT---
upper sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156251_T02 (Zea mays), 3'ss of exon 6
gtatattctacgtggaaattttggggttatccaagataattgtgttatattacagcttttcttagtgtagaacagtgttaatgttcag-ctcttact----gcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
||| | | | ||| | || | | | | | | || ||| |||| | | ||| | || | | |||||| | |||||| || || |||| || ||||||||||| ||||| || |||||||||||||||||||| || || ||||||| | || |||| | || || | |
ccatagcccataagtaaactc--aggctgtttg---tcactttcaaatgttattgcttaatatgatactgaatattgaggtttccaaatctcttattaacagcagAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCTATC
upper sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
gtatattctacgtggaaattttggggttatccaagataattgtgttatattacagcttttcttagtgtagaacagtgttaatgttcagct---cttactgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
| | || | | | | | || | | | | | | | | || || | || ||| |||| | | |||| | |||| | | || | || || ||||||||||||||||||||||| || ||||| ||||| || || |||||||| || | || || |||| | |||||
gagtcttatcagccatggtccaaaaggaagcccatactaccat---aaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
upper sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G873277_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------gtatattctacgtggaaattttggggttatccaagataattgtgttatattacagcttttct-tagtgtagaacagtgtt--aatgttcagctctta-ctgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
| || || | | | | | ||| | || | | | | | ||| ||| | | || ||| | | | || |||||| || |||| | | || | || || ||||||||||| |||||||||||||| ||||| ||||| || || || ||||| || || || | ||| ||||| | |||
gtacattcctatatttatttgagttacttagcagttcattggcatgaactcgtttgcatatactgtgttgcgtatcatc-tggaagggtgccaaatcttgtctcttggctaacacaattcttcatcttttctctcttatctacagAAAAGAAGGTTAATAACTCATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCGCATCAGGATGGCGCACTTGGATTTCCCTTGGGCTGTTCGA
upper sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------gtatattctacgtggaaattttggggttatccaagat----aattgtgtta-tattacagcttttcttagtgtagaacagtgttaatgttcagctctta-ctgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
| || || | | | | | | ||| | || | || | | | || | || ||| || | ||| |||| || |||| | | || |||| || ||||||||||||||||||||||| || ||||| ||||| || || || || || || || |||| ||| ||||| | |||
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
upper sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
--gtatattctacgtggaaattttggggttatccaagataattgtgttatattacagcttttcttagtgtagaacagtgtta-atgttcagctcttactgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
|| | | | | || | ||| |||| | || || || || || || | | | | || ||| || | || ||| | ||||| || || || || || ||||||||||| |||||||||||||| ||||||||||| || ||||| |||||| | || ||||| || |||||||||||||
tttcatcatgtggctccatataattttgttgatcaagttggttctgatac-ttgtagtttgtagattttgattgctgtcttatatctccatttctaa--acagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCACMapped 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|11412728|gb|BF424739.1|BF424739EST: GGGGAGTTCCAGTTCCAGAGGCCAATGCTGAACTGCAAGCAAATATTGAT AGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTT
genomic: GGGGAGTTCCAGTTCCAGAGGCCAATGCTGAACTGCAAGCAAATATTGATgtatgtctga ... cttactgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTT
EST:
gi|151397025|gb|EV266898.1|EV266898EST: GGGGAGTTCCAGTTCCAGAGGCCAATGCTGAACTGCAAGCAAATATTGAT AGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTT
genomic: GGGGAGTTCCAGTTCCAGAGGCCAATGCTGAACTGCAAGCAAATATTGATgtatgtctga ... cttactgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattacagcttttcttagtgtagaacagtgttaatgttcagctcttactgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
ctcttac putative branch site (score: 3)
ctcttact CT-rich tract
ttttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattctacgtggaaattttggggttatccaagataattgtgttatattacagcttttcttagtgtagaacagtgttaatgttcagctcttactgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - -ctacgtg
- - - - - - - - - - -tggggtt