Sequence
atgc intronic sequence ATGC exonic sequence...atagtggattttacaacaatagatagatgaattgtttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
Basic information
species | Glycine max |
transcript | GLYMA05G09460.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 5
-atagtggattttacaacaatagatagatgaattgtttgtagtt--gtatttgtttgagttttttttttctcacaaatc-tgtttgatggtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
| | | |||| |||||| | | | || || || | | | | |||| | | ||||| | || | | ||| ||||||||||| || |||||||||||||| || ||||| ||||| ||||| |||||||| || ||||| ||||||| |||| || |||||||||
taaatttcatttgcttacaatacac---tatactggcattactttaggacattatctggtttactctaataagcaaatgataaaagacaatctttttc-tgcagTCTTCAGTTCTCCATTCACAACCAAAATCCACTGTAGGAACCCCTGCTTATATTGCACCTGAAGTTCTGTTGAAGAAAGAATACGATGGCAAG
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 5
atagtggattttacaacaatagatagatgaattgtttgtagttgtatttgtttgagttttttttttctc---acaaatctgtttgatgg---tgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
|| | | | | | ||| || | | | | |||| | | | | || | | | || ||| | | | ||||| ||||| || || ||||||||||||||||| ||||| || |||||||| || ||||||||||||||||| ||| | || |||| || ||||| |||
-----actttctgtagtagtgaaaagaagagagaactttcgctagatttttctcgatgtgattgctgcctggataatattgtactgttgctttctgattt-tgcagTCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAG
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
---atagtggattttacaacaatagatagatgaattgtttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
|| || || || | | ||| |||| | ||| | |||| ||||| |||| | ||| | || | | ||||| || || |||||||| ||||| ||||||||||| ||||| ||||| |||||||| || ||||| |||||||| |||| ||||||||||||
ggcttaatgt-ttacacgatagtagtagaatgatgaatatgttcatagggttgtc--agtttccttttaactaacaataccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
---atagtggattttacaacaatagatagatgaattgtttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
|| || || || | ||| || | || | | | || | | |||||| |||| | ||| | || | | ||||| || || |||||||| || || ||||| ||||| ||||| ||||| |||||||| || ||||| ||||||||| |||| ||||||||||||
ggcttaatgt-ttacacgatggtagtagaataa--tgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
-----atagtggattttacaacaatagatagatgaattgt----ttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcc----cagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
| | |||||| | | | || | | |||| ||| | | | || | | | || |||||| | || ||| |||||||| || |||||||||||||||||||||||||| || ||||||||||| || |||||||| ||| || | || || ||||||||||||
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
-atagtggattttacaacaatagatagatgaattgtttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatg-gtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
| | | | | | | || || ||| || | || | ||||| | ||| ||| | ||| | | ||| || | || |||||||| || |||||||| ||||||||||||||||| || ||||||||||| ||||| ||||| | | | ||| || ||||||||||||
tcttatcgttcatgct-ctttacctacatgtgtttcctactaa-gtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------------------------------------------------atagtggattttaca----acaatagatagatgaat-tgtttgtagtt--gtatttgtttgagttttttttttctcacaaatctgtttgatg-gtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
| ||| | ||| | | || | || ||||| | || | ||||| | ||| ||| | ||| | | ||| || | || |||||||| || |||||||| ||||||||||||||||| || ||||||||||| ||||| ||||| | | | ||| || ||||||||||||
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
upper sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
atagtggattttacaacaatagatagatg---aattgtttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
| | | || || | || | | ||| | | | || | | | || || | | | | ||| ||| | | | |||||||| |||||||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| ||| ||||| || |||||||||
agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaa--atctgacagtggcactt-ctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAGMapped 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|7685757|gb|AW756405.1|AW756405EST: ATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATAT
genomic: ATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAGgtaaggtttt ... attcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATAT
EST:
gi|120495545|gb|EH223712.1|EH223712EST: ATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG TCTTCAGTGCTTTCATTCACAACCAAAGTCAACTG
genomic: ATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAGgtaaggtttt ... attcgcccagTCTTCAGTGCTT-CATTCACAACCAAAGTCAACTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
ttcgccc CT-rich tract
tttgagtttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagtggattttacaacaatagatagatgaattgtttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg