Sequence
atgc intronic sequence ATGC exonic sequencegtaactggaagtctggaacaattcatgactttctgattttgcttttatgccaatatctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
Basic information
species | Glycine max |
transcript | GLYMA08G02960.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 3
-------gtaactggaagtctggaacaattcatgactttc-tgattttgcttttatgccaatatctcacattt-tcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
| || || | | | ||| | | | || | | || ||||| | | |||||| | | |||| ||||||||||| || ||||||||||| ||||| ||||| |||||||||||||| || ||||||||||| || || ||||| || ||||||||||| ||
gttagtaatgacaagacattcatgtgcttagttaactcaagcggtgattctgtggaagccattgctcacttctgctctttcatgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTGCTGGCCTGAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 3
----gtaactgga--agtctg--gaacaattcatgactttctgattttgcttttatgccaatatctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
||||||| | | |||| | | || | || | || | | || | | || | ||| | | |||| |||||||||||||| ||||||||||| ||||| ||||||||||||||||| || |||||||||||||| || || ||||| || ||||||||||| ||
gttagtaactgaaccattctgctggttacctctagtagttgttatgtaaaaat-gtggtggcttacttccttatgttttgttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 3
----gtaactggaagtctggaacaattcatgactttctgattttgcttttatgc-caatatctcacattttcctttcaa----ctgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
||||||| | | || | || | | || | | | ||||| | | | | | | |||| |||||||||||||| ||||||||||| ||||| ||||||||||||||||| || |||||||||||||| || || ||||| || ||||||||||| ||
gttagtaactgaacaattctgctggtt-acctctagtagttgttatgtaaaaacgtggcggctcacttccttgtgttgtgtttttttgcagCGTACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 3
--------gtaactggaagtctggaacaattcatgactttctgattttgcttttatg-ccaatatctcacattttcctttcaactgtac--agCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
|| | | | ||| | | |||| | || | ||| || || | | | | ||| ||| | | ||||||||||||||||||||| ||||| || || || ||||||||||| |||||||| ||||||||||||||||| ||||||||||||||||||||||| ||
gttagtttgttgttatatatgtggtggagag-gtatctttattatctgtatttggtgattgattgtttatttggtgtttttgactttgcgtagCTTACTTCAATGATGCTCAAAGGCAAGCTACTAAGGATGCTGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATTAATGAACCTACTGCTGCTGCTAT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------gtaactggaa-gtctggaaca-attcatgactttctgattttgcttttatgccaatatctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
| ||| | | || | | || | ||||| || | || || | | | | || || |||||||||||||||||||||| ||||| || ||||| ||||| ||||| |||||||| ||||||||||||||||| || || ||||||||||||||||| ||
gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------gtaactggaagtctggaac---aattcatgactttctgattttgcttttatgccaatatctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
| || || || |||| || | ||| | | || | | |||| ||||| | |||| ||||||||||||||||||| ||||||||||| || || |||||||| || |||||||| || |||||||| ||||||||||||| || |||||||| || ||
gtgagtatcactcttctagatataacgtgtgaggttttgaactgcccgcttacactcttcttgaaatgtgaattagcattttgttcattaggatgttttactcatatta---gctttccatgcaacc-cgcagCTTACTTCAATGATGCCCAGAGGCAGGCTACAAAGGATGCTGGCGTTATTGCTGGCCTGAATGTTGCACGAATTATTAATGAGCCAACTGCTGCAGCTAT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
gtaactggaa---gtctggaacaattcatgactttctgattttgcttttatgccaatat--ctcacattt---tcctttcaactg-tacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
|||| || || || || |||| | | || |||| || | || || | ||| | ||| ||||| ||||||||||||||||||||| ||||||||||||||||| ||||| || | |||||||| || |||||||| ||||| || ||||||||||| || || |||||
gtaatgtaaaacagtttgatttgatggatgaagtaa-attgctgtttttctgttgagatgacttatgtttctattcttacaacttctacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCATMapped 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|120530199|gb|EH258333.1|EH258333EST: GGAAGCATTCCTTGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAG CTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTG
genomic: GGAAGCATTCCTTGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaa ... aactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttctgattttgcttttatgccaatatctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
atctcac putative branch site (score: 3)
ttttcctttcaact CT-rich tract
ttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactggaagtctggaacaattcatgactttctgattttgcttttatgccaatatctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC