Sequence
atgc intronic sequence ATGC exonic sequencegtgtgaggaaaatcaggaatttagatctacctattcattatcccttctttttttttgtattgggaaagggctggttcttgtttcaataatagcagttttgcaaccttgtaatgtttttgggttgctgattgcagTGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAATCAGCTTGATGGTTTTAGTAGTGATGACCGGATTAAG
Basic information
species | Glycine max |
transcript | GLYMA03G39500.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgtgaggaaaatcaggaatttagatctacctattcattatcccttctttttttttgtattgggaaagggctggttcttgtttcaataatagcagttttgcaaccttgtaatgtttttgggttgctgattgcagTGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAATCAGCTTGATGGTTTTAGTAGTGATGACCGGATTAAG
| | ||||| || ||| | | | | | | | | ||| | | | | | || || ||||| || | ||||||||| || ||||||||||| || ||| | || ||||| || ||||||||||| ||||| || || ||||| ||||| || ||||||
----------------------------------------gtacaaatctttttctg-attccaa-----ttcatgtatttctgcactttctcagctatttgctcaaatcacattctttggttga-gagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgaggaaaatcaggaatttagatctacctattcattatcccttctttttttttgtattgggaaagggctggttcttgtttcaataatagcagttttgcaaccttgtaatgtttttgggttgctgattgcagTGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAATCAGCTTGATGGTTTTAGTAGTGATGACCGGATTAAG
| | || | ||||| |||| | || | || | | || ||| ||| | | | || | ||||| | || | ||| || || | ||||||||||||| |||||||| |||||||| ||||| |||||||| || || | |||||||||||||| ||||| |||||||| || || |||
----gtaaaccattattggtttagcactacatctttcatgatatttttatcaaaatggatttggattgaaattatcaaggtgaactcatgagcagcctccttgactatagacttttctgcctt--ttattgcagTGAAGTGAGTGGAGATAGGGAGGTGCAGCGGACAATGTTGGAGTTATTGAATCAGCTTGATGGCTTTAGCAGTGATGATCGCATAAAG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 6
gtgtgaggaaaatcaggaatttagatctacctattcattatcccttctttttttttgtattgggaaagggctggttcttgtttcaataatagcagttttgcaaccttgtaatgtttttgggttgctgattgcagTGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAATCAGCTTGATGGTTTTAGTAGTGATGACCGGATTAAG
| | || |||| || | | | ||| || || | | ||||||||| || || || |||| || || || || ||| | || | | ||||||||||||||||| ||||| || ||||||||||||
--------------------------------------------------------------------------gtttggtctcaa-aacggacaccggccggtttactaacag---tgacttaca---tacagTGAAGTTAGCGGTGATCGGGAAGTCCAACGGACCATGCTTGAGCTTTTAAATCAGCTTGATGGTTTCAGTAGCGACGACCGGATTAAG
upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 6
gtgtgaggaaaatcaggaatttagatctacctattcattatcccttctttttttttgtattgggaaagggctggttcttgtttcaataatagcagttttgcaaccttgtaatgtttttgggttgctgattgcagTGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAATCAGCTTGATGGTTTTAGTAGTGATGACCGGATTAAG
| | || |||| | || | | || | || || | | ||||||||| || || || |||| || || || || ||| | || | | ||||||||||||||||| ||||| || ||||||||||||
--------------------------------------------------------------------------gtttggtctcaaaacggacacggccgg-----tttactaacagtgacttaca---tacagTGAAGTTAGCGGTGATCGGGAAGTCCAACGGACCATGCTTGAGCTTTTAAATCAGCTTGATGGTTTCAGTAGCGACGACCGGATTAAGMapped 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|209727654|gb|BW663794.1|BW663794EST: ATAGATGAAATTGATGCAATTGGAACAAAGCGTTTCGATAG TGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAA
genomic: ATAGATGAAATTGATGCAATTGGAACAAAGCGTTTCGATAGgtgtgaggaa ... ctgattgcagTGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAA
EST:
gi|209718166|gb|BW657812.1|BW657812EST: ATTATATTTATAGATGAAATTGATGCAATTGGAACAAAGCGTTTCGATAG TGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAA
genomic: ATTATATTTATAGATGAAATTGATGCAATTGGAACAAAGCGTTTCGATAGgtgtgaggaa ... ctgattgcagTGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAA
EST:
gi|16281884|gb|BI944719.1|BI944719EST: ATTATATTTATAGATGAAATTGATGCAATTGGAACAAAGCGTTTCGATAG TGAAGTAAGTGGA
genomic: ATTATATTTATAGATGAAATTGATGCAATTGGAACAAAGCGTTTCGATAGgtgtgaggaa ... ctgattgcagTGAAGTAAGTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttcaataatagcagttttgcaaccttgtaatgtttttgggttgctgattgcagTGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAATCAGCTTGATGGTTTTAGTAGTGATGACCGGATTAAG
tgctgat putative branch site (score: 3)
taatgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgaggaaaatcaggaatttagatctacctattcattatcccttctttttttttgtattgggaaagggctggttcttgtttcaataatagcagttttgcaaccttgtaatgtttttgggttgctgattgcagTGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAATCAGCTTGATGGTTTTAGTAGTGATGACCGGATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT