Sequence
atgc intronic sequence ATGC exonic sequence...gtgttgtccaacaaatatgtcaatccattcatttataatatttttgaattttttgttcacgtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
Basic information
species | Glycine max |
transcript | GLYMA13G28720.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 4
-gtgttgtccaacaaatatgtcaatccattcatttataatatttttgaattttttgttcacgtgtcatgaatgctcattgttagttttttatt---ctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
|||| |||| ||| || | | | | || | | ||| |||| || | | |||| ||||| | || || | ||| ||||| || |||| || ||||| ||||||||||| |||||||| || ||||||||||| |||||||||||||| || |||||||| |||||||||| |||
ttctttgtgattaaaatgagtccgtc-acagactcgtgcaatctcatcagtttatgttaac---tactaaatgatcattatattcttgttggtttacttgacagGCATAAAAGGAAAGATGAGAGATTACCAACTAGCTGGACTTAATTGGCTCATACGCTTGTATGAGAATGGCATCAATGGAATATTGGCTGATGAGATG
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 4
--------gtgttgtccaacaaatatgtcaatccattcatttataatat-ttttgaattttttgttcacgtgtcatgaatgctca-ttgttag---------ttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
| | |||| ||| | | | | | | | ||| | | || |||| | | ||||| | | |||||| | |||| | || | ||||||| | ||||| ||| | || |||||||| ||||| || || ||||||||||| ||||| |||||||| || ||||| || ||||||||||||||
gtgagctcctttcccttcacaattatttgtaactgtatcataagagtatgctgccaccattctgttaatataagttgaataataaattgttaaaatgtaatatattttttgctctgcagGTATAAAGGGGAAGATGCGAGACTACCAACTAGCTGGGCTTAATTGGCTCATACGGTTGTACGAGAATGGTATCAATGGTATATTGGCTGATGAAATG
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 1
gtgttgtccaacaaatatgtcaatccattcatttataatatttttgaattttttgttc---acgtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
||||| |||| | || ||| |||| || ||||||| || | ||| | || | | | | ||| | | | | |||| ||| | || || ||| | |||||||| |||||||||| || ||||| |||||||||||||||||||| || ||||| || | |||||||| |||
---gaaaccaaccaataatttttggttttagttttcttaggttttatatcctttgttccttttgtcttatgtaaacttttattaaatgtttgaatttctccagGCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 4
gtgttgtccaacaaatatgtcaatccattcatttataatatttttgaattttttgttcac-gtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
| | | || | || || ||| ||| ||| |||||||| | | ||| | | | | | | ||| | ||||| |||| ||| | || || ||| | ||||| ||| | |||||||| || ||||| |||||||||||||||||||| || ||||| || | |||||||| |||
-tctcatggaaaccaatcaataaggttttagttttcttgggccttgtattctttgttcattgctttatgtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgttgtccaacaaatatgtcaatccattcatttataatat--ttttgaattttttgttcacgtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
|| | ||| || | | || || ||| || | | | | | || | | ||| |||| | || || | |||||||| |||||||| ||||| ||||||||| | ||||| | ||||||||||| || | ||||||||||| |||||||||||||| ||||||||||||
-cgtaaccatacatatttttgtgacctcacagttagtatgtagtatagcgtaaattactgggaaagcttgag-attcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 4
--gtgttgtccaacaaatatgtcaatccattcatttataatatttttgaattttttgttcacgtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
|| | | | || | || || || || || || | | | | || || || || | | | || ||||||| || ||||| | || ||||||||| | ||||| ||||||||||||| || |||||||||| || |||||||| ||||| || |||||||||
gtttgatatattcttcagttgcgagctcacaatttctaggtaggactgcataaattctgtagaatttagagat-ctgatc-ttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
gtgttgtccaacaaatatgtca-atccatt-catttataatatttttgaattttttgttcacgtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
| || | | | | | || |||| || || | | | | | || ||||| | | | | ||| || | ||||||| || || || ||||| ||||||||||| ||||| ||||||||||||||||| ||||||||||||| || |||||||| || || |||||||||
-ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgtt-gtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATGMapped 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|207840357|gb|GD813140.1|GD813140EST: AGGAGAAGAAGATGGTCTAGCAAACACACGTCTGGTGACACAACCATCAT GTATCCAAGGGAAAATGAGGGATTACCAACTGGCTAGGACTA
genomic: AGGAGAAGAAGATGGTCTAGCAAACACACGTCTGGTGACACAACCATCATgtaagtgttt ... ttctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCT-GGACTA
EST:
gi|254345541|gb|GR851703.1|GR851703EST: AGGAGAAGAAGATGGTCTAGCAAACACACGTCTGGTGACACAACCATCAT GTATCCCAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCA
genomic: AGGAGAAGAAGATGGTCTAGCAAACACACGTCTGGTGACACAACCATCATgtaagtgttt ... ttctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattttttgttcacgtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
ttttttattctttac CT-rich tract
attgttagttttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttgtccaacaaatatgtcaatccattcatttataatatttttgaattttttgttcacgtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - -ccaacaa
- - - - - - - - - - - - ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgct