Sequence
atgc intronic sequence ATGC exonic sequencegtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgtgagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
Basic information
species | Glycine max |
transcript | GLYMA18G03870.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgtgagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
| | || || || ||| | ||| | | || || | || |||| | | || || |||| |||| ||| | || ||||||| |||| || || ||||||||||||||||| || |||||||| || || ||||||||||||| || | || |||||||| |||| | ||
-------------------------------------------------------gtagcctacattttgcactaacactatggc----actacatttgctgggctagggaactttgctgattaaaactaa---atgt------------tttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------
upper sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g62810.3 (Oryza sativa), 3'ss of exon 2
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgtgagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
| | || || || ||| | ||| | | || || | || |||| | | || || |||| |||| ||| | || ||||||| |||| || || ||||||||||||||||| || |||||||| || || ||||||||||||| || | || |||||||| |||| | || || ||
-------------------------------------------------------gtagcctacattttgcactaacactatggc----actacatttgctgggctagggaactttgctgattaaaactaa---atgt------------tttctcgaaagcttcagATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCCGTGCAT
upper sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g38270.2 (Oryza sativa), 3'ss of exon 5
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgt---gagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
||| ||| | | | | | | | | | | | ||| || | | |||| |||| | | | ||| || | | || ||||||| | || ||||| |||||||||||||||||||| ||||| || || ||||| || ||||| || || | || ||||| || |||| | |||||| |
------------------------------------------------------------------------gtaa-cttatattgggcgtttactgctgtattctcttcacactcaactaggttaggtaag-catgctgatcagcgaaatattttctccaaagcttcagATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACCTTGTGT
upper sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgt---gagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
||| ||| | | | | | | | | | | | ||| || | | |||| |||| | | | ||| || | | || ||||||| | || ||||| |||||||||||||||||||| ||||| || || ||||| || ||||| || || | || ||||| || |||| | ||
------------------------------------------------------------------------gtaa-cttatattgggcgtttactgctgtattctcttcacactcaactaggttaggtaag-catgctgatcagcgaaatattttctccaaagCTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC------
upper sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttat--ggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgt------gagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
| | | || | ||| || || | | | ||| | |||| | | ||| | ||| || | | | ||||||| |||| ||||||||||||||||| ||||| || |||||||| || ||||||||||||||||| |||| || || ||||| |||| || || || ||
-----------------------------------------------------------------------------------------gta-acctgcatatgtcattatgacactgacatttgccctataaggatatttactgactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
upper sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G302245_T01 (Zea mays), 3'ss of exon 3
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgtgagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
| || || | | | ||| | || |||| |||||| | | | | |||| | |||| || | || ||||||| |||| ||||| ||||||||||| ||||| || |||||||| || ||| |||| |||||||| |||| || || ||||| |||| || || || ||
----------------------------------------------------------------gtaatctg-catttgtcattatgacactgacattttccctgtatggatatttactga------ctaaaatatgt-------------ttcttcgaagcttcagATTTAGGTCAGGTATGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTCTGGGCTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
upper sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgt--gagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
||| | | || ||| || | | ||| ||| | || || | || ||| | || | | || || | | || | || || | | | ||| || | || | || || ||||||| | | || | ||||||| |||||||||||||||||||| ||||| || ||||| |||||||| ||||| ||| | |||| | || ||||||||||||| |||| || ||
------gtgagatttttagct-tttcacacaccatgtcactaatgaggtacattggtt--atcaattatg-aaaaaaatatcagt---ggcggtatccattaagctaaagagcttttggtgtgctataataatcacttgatgcatcctaattttttttctgaagtccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT
upper sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
--gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatctt---ttggttgaagcagaactt---tttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaat-tttctgtgagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
|| | || || | | || ||| |||| | || | ||| || | || | | | || |||| | || | || || | | | | | ||||||| || || || || || | | | || || || | || | |||||||||| | |||||||||||||||||||||||||| ||||| ||||| || ||||||||||| | ||||| ||||| ||||||||||||| || |||||| |
gtaaatccatgaaatcttggattgtt-gtc--cctaagcctcagttttaattcatagttctt-tttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctattgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGTMapped 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|11688812|gb|BF596488.1|BF596488EST: AAGGATAGCAAGTGTAGCTGCTGGTGGTCGCCATACCTTAGCATTGTCAG ATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTCGGTT
genomic: AAGGATAGCAAGTGTAGCTGCTGGTGGTCGCCATACCTTAGCATTGTCAGgtattgactt ... tgagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcagttatgcaatctaagacatgtcattgattgtaattttctgtgagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
cattgat putative branch site (score: 4)
ttttctgt putative PPT
attgattgtaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgtgagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC