Sequence
atgc intronic sequence ATGC exonic sequence...cacttagtgttctatataaagcgtaaggcacttgttatgttgtcatgataatggggtgctgtacaaccttgctgaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
Basic information
species | Glycine max |
transcript | GLYMA18G43020.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
-cacttagtgttctatataaagcgtaaggcacttgttatgttgtcatgataatggggtgctgtacaaccttgctgaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
|| || | | | || | || |||| | || | || || | | || | || | | | | ||| ||||||||| |||||||| ||||||| ||||| || ||||| |||||||||||||| ||||| || ||||| ||||| || | ||||| || ||||||||
tttgttggtttcatcaaccttgcttcctccataacatatgcatacctgctgattatctgttaattttctccactaagaggccatctaaaat-cttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
cacttagtgttctatataaagcgtaaggcacttgttatgttgtcatgataatggggtgctgtacaaccttgctg--aaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
|| | ||| || | | | |||| || | | || | | || | || || | | | || | | | || | | ||||||||| |||||||| |||| || ||||||||||| || |||||||||||||| || || |||||||| ||||||||| | || ||||| ||||||||
ca-tgagtattgactgcctatttttgtcgacttcacatttcatgatagtcctctatccctct-taatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 11
cacttagtgttctatataaagcgtaaggcacttgttatgttgtcatgataatggggtgctgtacaaccttgctg--aaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
| | || | ||| | | || | || | || |||| | | | || || || | | || | || || | | ||||||||| |||||||| |||| || |||||||| ||||| ||||||||||| || || || || ||||| ||||| ||| | || ||||| ||||||||
-tttgattggtttatttggctgctgagctttgtcttcgtatttcgtgatcgaaaaatcatct-taatctaactaccatacttttcctgccatatgtgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAG
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
cacttagtgttctatataaagcgtaaggcacttgtt-atgttgtcatgataatggggtgctgtacaaccttgctgaaagttctattgttttacct---tttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
| | | || | | | | | || ||| | ||| | | | ||| | | | || | || || ||||||||| || |||||| |||| ||||||| || ||||||||||| || || || ||||| |||||||| ||||||||| |||| ||||| || |||||
--gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------cacttagtgttctatataaagcgtaaggc---acttgttatgttgtcatgataatggggtgctgtacaaccttgctgaaagttc---------tattgtt-ttacct-------tttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
| || | | | | | |||| ||| | |||| | | | | | |||||| | | ||| |||||| || || |||||||||||| || |||||| |||||||||||| |||||||||||||||||||| || |||||||||||||| ||||| |||| ||||| ||||||||||
gtttgcatgtttagtcctctaaattcattaacagatataattgggttgggaccagcaccacaaggggggactcttactgttattttatgtagaatatatttccagaccttggtagatgtttatctataatcattgttgttggctcctccaatttcagTGTGATTCAATTCTGCGCCACAGCATTTGGTTACTATGCTCAAGCAACTGCTGCACAGGAAATATTTGGCCACACACTGGAATCTCTCAAAGGAATTAAA
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ37798 (Selaginella moellendorffii), 3'ss of exon 11
cacttagtgttctatataaagcgtaaggcacttgt-tatgttgtcatgataatggggtgctgtacaaccttgctgaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
|| | | ||| ||| | | | | | ||| || || || | || | ||||||||||||||||||||| | ||||||||| | ||||| | ||||| |||| || ||||||||||||| || | ||||| ||||| ||||| ||
---------------------------------gtatgcactatcaagattcttagct--ttcaaaactcc-----aacttggat---acaaactctccagTGTGATCCAGTTCTGCTCTAAAGCATTTGCATTGTATGCGCGTGCAACCACAGCTCAAGAAATATTTGGTCTTACACTTGAGTCCCTTCGTGGAATCAAG
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ32053 (Selaginella moellendorffii), 3'ss of exon 11
cacttagtgttctatataaagcgtaaggcacttgt-tatgttgtcatgataatggggtgctgtacaaccttgctgaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
|| | | ||| ||| | | | | | ||| || || || | || | ||||||||||||||||||||| | ||||||||| | ||||| | ||||| |||| || ||||||||||||| || | || || ||||| ||||| ||
---------------------------------gtatgcactatcaagattcttagct--ttcaaaactcc-----aacttggat---acaaactctccagTGTGATCCAGTTCTGCTCTAAAGCATTTGCATTGTATGCGCGTGCAACCACAGCTCAAGAAATATTTGGTCTTACACTTGAATCCCTTCGTGGAATCAAGMapped 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|22522977|gb|BU081788.1|BU081788EST: ATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAG TGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
genomic: ATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAGgtcagtatgt ... accttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgataatggggtgctgtacaaccttgctgaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
ttgttttaccttttc CT-rich tract
tattgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacttagtgttctatataaagcgtaaggcacttgttatgttgtcatgataatggggtgctgtacaaccttgctgaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- cttagtg
- - - - - - - - - - - - - - cacttgt
- - - - - - - - - - - - - - - - - - -tgttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - -tggggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtaca