Sequence
atgc intronic sequence ATGC exonic sequence...cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
Basic information
species | Glycine max |
transcript | GLYMA15G15310.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 12
---------------------------------------------cttcttgaccgtatttaactcttaccttt--ttctctagttgcattgctgttctttacttgctttattgttt---------actaactacttttaagctgt---tttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| | | | ||| | ||| | | | || |||| | | || | | | ||| || | | | | | | || | ||| | ||| |||| ||| |||||||||||||||| || || |||||||| ||||| || |||||||||||||| ||||||||||||||||| || || || || | |
gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaatgatgagacatgaactctacttttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 12
----------------------------------------------------------------------------cttcttgaccgtat-ttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
||||| | | || | | | | || || | |||||| ||| || || || || | | || | || || | | |||| |||||||||| ||| |||||||||||||||| || || || || || || || || ||||| |||||||| ||||||||||||||||| ||||| || || |||
gtatacatgtttttagtttgtgccacttatttctatcagttttttttccttgcagggttatttctatcagttgtgttgtcttgtctccaaattggcacctgggtattgctgtc-ttgcatggct--tcattcagtgacatactttgggcttgacaattgtatgttcctttc-tgcagTTGATTTACCGGCCTGACACTGGAGAAATTCTTGGTGTGCACATTTTGGGTTTGCACGCTGCTGACCTCATCCACGAGGCATCAAATGCCATTGCCCTAG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
--------------------------------------------------------cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
||| | || | | | |||| | |||| || | | | | | | | | | | || | | || |||| ||| |||| || | |||||||| ||||| || || ||||||||||| || || ||||||||||||||||||||||| |||||||| ||||| || || | |
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatg---ctagggagcctg-tatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 12
--cttcttgaccg-tatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaa--ctacttttaagctgttttca-tgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| | || | || || || | | |||| | | | |||||||| ||| | || || | | || | || ||| |||||||||| ||| | |||||||| || || || || || ||||| || || || |||||||||||||||||||| ||||||||||| ||||| || || |||
gtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttt-tcattaacagaatttgacaatatgtggtcctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G152958_T02 (Zea mays), 3'ss of exon 12
--cttcttgaccg-tatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaa--ctacttttaagctgttttca-tgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| | || | || || || | | |||| | | | |||||||| ||| | || || | | || | || ||| |||||||||| ||| | |||||||| || || || || || ||||| || || || |||||||||||||||||||| ||||||||||| |
gtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttt-tcattaacagaatttgacaatatgtggtcctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAA---------------
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
cttcttgaccgtatttaactcttacctttttctc---tagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatg----cagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| || | || || | |||||| || ||||| | | ||| | | | || | | || | |||||| ||| |||||||||| ||||||| ||| || || || ||||||||||||||||| ||||||||||||||||| ||||| || ||||| || || || || ||||
-gtgaagagaagaaccaaaaattgaaataaaaaaagatagttgtat-atagttctggagtgacttg--cgaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 12
cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| | | | || | || | || | || || | ||||| | || || | | || || || || || |||||||||| ||| |||| || || || |||||||||||||||||||| ||||| || || || || |
------------------------------------------------gtaataaaataattcgtcgtaacacggttgatt--gatttgattcc-tgcagCTTATTTATCGCCAAGATACCGGGGAAATCTTGGGAGTTCACATAATTGGCTTACACGCAGCTGATCTCATCCACGAGGCTTCCAACGCCATGGCTTTGG
upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 12
cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| | | | || | || | || | || || | ||||| | || || | | || || || || || |||||||||| ||| |||| || || || |||||||||||||||||||| ||||| || || || || |
------------------------------------------------gtaataaaataattcgtcgtaacacggttgatt--gaattgattcc-tgcagCTTATTTATCGCCAAGATACCGGGGAAATCTTGGGAGTTCACATAATTGGCTTACACGCAGCTGATCTCATCCACGAGGCTTCCAACGCCATGGCTTTGGMapped 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|5509415|gb|AI855973.1|AI855973EST: NAGCT-ACACAAAGGCCTTAGCTGAAACCGAAGCGTAGGGTCTTGCCAAG TTGATATACAGGCCTGACACTGCAGAGATACTGGGAGTTCATATATTTGGG
genomic: AAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGGAGGGTCTTGCCAAGgttatatttc ... tttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGG
EST:
gi|19054208|gb|BM732875.1|BM732875EST: AAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGGAGGGTCTTGCCAAG TTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGG
genomic: AAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGGAGGGTCTTGCCAAGgttatatttc ... tttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
tactaac putative branch site (score: 0)
ctgttttc putative PPT
tttattgtttactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
cttcttg
- - - - - - - - - - - - - - - - - - - - -attgctg