Sequence
atgc intronic sequence ATGC exonic sequenceTGATATTGGAGCTCTTGAAAATGTCAAGGATACTTTGAAGGAATTGGTTATGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgtttactttacagattgaaacacattctatcatttaacatgcattctctgtgtctattgacagtaggagttagattccattgttgttgctgataaaaaaa...
Basic information
species | Glycine max |
transcript | GLYMA04G37050.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 5'ss of exon 21
TGATATTGGAGCTCTTGAAAATGTCAAGGATACTTTGAAGGAATTGGTTATGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgtttactttacagattgaaacacattctatcatttaacatgca--ttctctgtgtctattgacagtaggagttagattccattgttgttgctgataaaaaaa---
|| |||||||| || |||||||||||||| |||||||||||| | || |||||||| || || |||||||| | || | |||||| ||| | | ||||| | | | | ||| || ||| || | | || | ||||| || | | || | | | | | | || |
GGACATTGGAGCACTAGAAAATGTCAAGGAAACTTTGAAGGAACTAGTGATGCTTCCGTTGCAAAGGCCCGAATTGTTCTCCAAAGGACAACTTATGAAGgt--agctcaagcttcataac---ttttatttagtacccttcagttcctctgcactctgtgtgatctttcttcagtcttccgtatcacttgtagaaatttgatgt
upper sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 21
TGATATTGGAGCTCTTGAAAATGTCAAGGATACTTTGAAGGAATTGGTTATGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgtt-------tactttacagattgaaacac-attctatcatttaacatgcat-tctctgtgtctattga-cagtaggagttagattccattgttgttgctgataaaaaaa
||||||||||| | |||||||||||||| |||||| |||| || |||||||||||||| || ||||| ||| | || | |||||| ||| | | ||||| | || || | ||||| | || | | | || ||| | ||| || | | | || | | | | ||| || | | ||
GGATATTGGAGCATTAGAAAATGTCAAGGAAACTTTGCAGGAGTTAGTTATGCTTCCTTTGCAAAGGCCTGAGTTGTTCTCCAAAGGACAACTTATGAAGgtactggccattctctaaactttgaagtgtgaccctcttgaaaacctaatatatctgtatgtttagtaatccataagggcttg-ttcggttctacc--ccaat-------
upper sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 20
TGATATTGGAGCTCTTGAAAATGTCAAGGATACTTTGAAGGAATTGGTTATGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgt--ttactttaca-------gattgaaacacattctatcatttaacatgcattctctgtgtcta-ttgacagtaggagttagattccattgttgttgctgataaaaaaa
||| ||||| || ||||| |||||||| || ||||| |||||| |||||||||||||||| || |||| || || || ||||| ||||||||||| ||||| || ||| | || | | |||| ||| || ||| || | |||| || | || | || || |
TGACATTGGGGCACTTGAGAATGTCAAAGACACTTTAAAGGAACTGGTTATGCTTCCTTTTCAATGGCCTGAACTTTTCTGCAAGGGGCAATTAACAAAGgtggttgtcttatccgcatttggttttaggaaattcccatattgtttcactatgtcctgcctcgaattgatgacagatctgtgaaggaccttttatttgt----------
upper sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 20
TGATATTGGAGCTCTTGAAAATGTCAAGGATACTTTGAAGGAATTGGTTATGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgt------ttactttaca----gattgaaacacattctatcatttaacatg--cattctctgtgtctattgaca--gtaggagttagattccattgttgttgctgataaaaaaa
||| ||||| || ||||| || ||||| |||| || |||||| ||||||||||||||||||| |||| || || || ||||| ||| ||||||| ||||| | || | || | || | | | | | || |||| | | | | | | ||| ||| || | || || || | |
TGACATTGGGGCACTTGAGAAAGTCAAAGATATCTTAAAGGAACTGGTTATGCTTCCTTTACAACGGCCTGAACTTTTCTGCAAGGGGGAATTAACAAAGgtggttctcttctctgcattatgtttcagaaaactcccataattttttgaggtcctgcctcggatttatcacagatgtatgaaggaaataccttttattt--------------
upper sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 21
TGATATTGGAGCTCTTGAAAATGTCAAGGATACTTTGAAGGAATTGGTTATGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgtttactttacagattgaaacacattctatcatttaacatgcattctctgtgtc-tattgacagtaggagttagattccattgttgttgctgataaaaaaa---
||||||||| || || |||||||||||||| || |||||||| ||||| |||||||| |||| ||||| || || |||||||| ||||||||||||||||||| | | || | || | || | ||| || | ||| || | || ||| | || | | || ||||| |
TGATATTGGGGCCCTGGAAAATGTCAAGGACACATTGAAGGAGTTGGTGATGCTTCCACTACAAAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAGgttttcac-atctgttcattttcagcttgg-atgtgctccttgttcaaagtataatatggataataattgttgg--tctactttttttgctctttggctcctttMapped 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|16283953|gb|BI945829.1|BI945829EST: TGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAG N
genomic: TGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgtttacttta ... ttccatgcag-
EST:
gi|16283953|gb|BI945829.1|BI945829EST: TGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAG N
genomic: TGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgtttacttta ... ttccatgcag-
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGATATTGGAGCTCTTGAAAATGTCAAGGATACTTTGAAGGAATTGGTTATGCTTCCTTTACAGAGGCCCGAGCTATTTTGCAAAGGGCAATTAACCAAGgtttactttacagattgaaacacattctatcatttaacatgcattctctgtgtctattgacagtaggagttagattccattgttgttgctgataaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaaa