Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgatgatgattaatgaggtaggcacattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
Basic information
species | Glycine max |
transcript | GLYMA08G04840.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
gtaagt-ttcttgttctgtta--------tgaaaatgtag-attgatagagaatatgatgatgattaatgaggtaggcacattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
||| || |||| || || | | | | |||||| | || | || | || ||||| |||| | | || | | | |||||||||||| |||||||||||||||||||| || ||| | ||||||||||| ||||||||||||||| ||||| || |||||||| | ||||||| |
gtacgtattctcgtcctataacttggcgttaagaatgtactactggtgaag--cagcattgtgatttgtgagtaacctgctgtg-gccgcgtgt--agGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
upper sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
--------------------gtaagtttct-tgttctgttatgaa----------aatgtag-attgatagagaatatgatgatga----ttaatgaggtaggcacattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
| | ||| |||||| || || ||||||| | | || || ||| | ||| || || | | | | | || | | ||||||||| ||| |||||||||||||||||||| || ||| | ||||||||||| ||||||||||||||| ||||| | |||||||| | ||||||| |
gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtgg-cagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
upper sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
------------------------------gtaagtttct-tgttctgttatgaaaatgtagattgatagagaa-tatgatgatgattaatgaggtaggcacattgtgttgtttact--cagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
| | | ||| | | | | | |||| | ||| | || | | | |||| || || | |||||||| ||| |||||||||||||||||||| || ||| | ||||||||||| ||||||||||||||| ||||| | |||||||| || ||||||| |
gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G455642_T02 (Zea mays), 3'ss of exon 1
--------------------------------------gtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgatgatgattaatgaggtaggcacattgtgttgtttact-cagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
| | | || |||| | | | || | | | | | || || | | | ||| | || ||| ||| ||||||||| ||| || |||||||||||||| || || ||| | ||||||||||| || |||||||||||| ||||| | |||||||| || ||||||| |
gtctgtctctctctctctttcagtaatccctcccattcatgcgcacaccatcctcgtatgcgtacgca---cgagcgc-attgcgtcagtaatgaac-acgcacgcatgctctgctgtgcactgcagGTGGACCTGACGGGCGGGTACTACGACGCGGGCGACAACGTGAAGTTCGGGTTCCCTATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G455642_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------gtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgatgatgattaatgaggtaggcacattgtgttgtttact-cagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
| | | || |||| | | | || | | | | | || || | | | ||| | || ||| ||| ||||||||| ||| || |||||||||||||| || || ||| | ||||||||||| || |||||||||||| ||||| | |||||||| || ||||||| |
gtacggacgggagtctgtctctctctctctttcagtaatccctcccattcatgcgcacaccatcctcgtatgcgtacgca---cgagcgc-attgcgtcagtaatgaac-acgcacgcatgctctgctgtgcactgcagGTGGACCTGACGGGCGGGTACTACGACGCGGGCGACAACGTGAAGTTCGGGTTCCCTATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgatgatgattaatgaggtaggc-acattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
|||||| | | | || || | | | | | | | | | | || ||| | | | ||| | ||||||| ||||| || || |||||||||||||| || ||||| |||||||| ||||||||||||||||| || |||||||| || ||||| | |||||||
gtaagtctactctactaacat-acatttcaaacttctc---cttcttctaatctctaacttttccgacgatatttcaaaaat--ctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT
upper sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------gtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgat--gatgattaatgaggtaggcacattg----------tgttg----tttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
| || || ||| | ||| |||| | | | || || | ||| | | | |||| || || || ||||| || ||||||||||||||||||||||| || || ||| | ||||||||| |||| ||||| |||| | ||| |||| ||| | | | | || |
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
upper sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgatgatgattaatgaggtaggcacattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
|| ||| | || || | | | || | || | | | | || | ||| | | |||||||| | | | ||||| |||||||| | || || ||| | ||||| || || |||||||||||||||| ||| ||||||||||||||||| | || |
----gtaccttagaatcttttgctcgtttgaaatgttt---ttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
upper sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ08014 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgatgatgattaatgaggtaggcacattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
|| | | | || || | | | || | || | | | | || | ||| | | |||||||| | | | ||||| |||||||| |||| || ||| | ||||| || || |||||||||||||||| ||| ||||||||||||||||| | || |
----gtaccatagaatcttttgctcgtttgaaatgttt---ttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCCGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAATMapped 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|18041520|gb|BM309814.1|BM309814EST: GCCTCCGCTGGCGCCACGACTCTGCATTGCACGACGGCGCCACCGCCGGA GTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGG
genomic: GCCTCCGCTGGCGCCACGACTCTGCATTGCACGACGGCGCCACCGCCGGAgtaagtttct ... gtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatagagaatatgatgatgattaatgaggtaggcacattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
gattaat putative branch site (score: 3)
tttactc putative PPT
atgattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgatgatgattaatgaggtaggcacattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG