Sequence
atgc intronic sequence ATGC exonic sequence...tctctggcatttcctttaaaaaaaaaaagaaagaaaaaaactaaacaatgaagctgcatgagatgattgtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA
Basic information
species | Glycine max |
transcript | GLYMA06G06310.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 1
tctctggcatttcctttaaaaaaaaaaagaaagaaaaaaactaaacaatgaagctgcatgagatgatt--gtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA
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--gggagtgttagtttcgaatatctgtatatagccattgacagagaattcgtttctgttattattacctgatattgttgttcttcttgtgttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g56450.1 (Oryza sativa), 3'ss of exon 1
tctctggcatttcctttaaaaaaaaaaagaaagaaaaaaactaaacaatgaagctgcatgagatgattgtgacacagtttgttttgaattgtatttat-agTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA
| || | | | | | | ||| | || | | || | | | | || | | | | | ||| || || ||| | || || |||||||||||||| ||||| ||||| || || |||| |||||||| ||||| |||||||||||||| ||||||||| |
-aatcaacgttgtcatggtagcttgattttatggtgtaaatgcagttattaggactgttgctctcctatttgctcaacatttctcattctttttttgccagCCAGAATGGTAAGTTTAGCTATGGGTATGCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAG
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 1
tctctggcattt--cctttaaaaaaaaaaagaaagaaaaaaactaaacaatgaagctgcatgagatgattgtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA
| ||||| | | | ||| | | | | | | || | |||| | | | | | || | || | ||| | || | || ||||| ||||||||||| || ||||||| || || |||||||||| ||||| || ||||| ||||| |||||||||||||| ||
--taacacatttgattgtcacacgaaattaagtgcactggagtccatgattttagattttgcgtatgactaattaataaatgttccccttttctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAG
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 1
tctctggcatttcctttaaaaaaaaaaagaaagaaaaaaactaa-acaatgaagctgcatgagatgattgtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA
| | || | ||| ||| | ||| | |||| | || || || | | |||| || || | || | | || || ||| | | ||| |||||||| ||||| ||||| ||||| || || | || |||||||| || |||||||||| ||||||| ||||||||||| |
-ttgttacagtagcttggctccaaatatcaaatcagtggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgccagCCAGAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAG
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G056572_T01 (Zea mays), 3'ss of exon 1
tctctggcatttcctttaaaaaaaaaaagaaagaaaaaaactaa-acaatgaagctgcatgagatgattgtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA----
|| | ||| ||| | ||| | |||| | || || || | | |||| || || | || | | || || ||| | | ||| |||||||| ||||| ||||| ||||| || || | || |||||||| || |||||||||| ||||||| ||||||||||| |
-----tacagtagcttggctccaaatatcaaatcagtggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 2
--------tctctggcatttcctttaaaaaaaaaaagaaagaaaaaaacta-aacaatgaagctgcatgagatgattgtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA
| | ||| ||| | || | | ||| |||||| | |||| ||| | | ||| ||| || || |||| | | ||||| ||| | || |||||||| || |||||||| ||||| || || || |||||||||||||||||||||||||||||||||||||||||||| || ||
ttgaggaccttataatgtttggttttatctttctaatat------catctacaacaataagagtgcacaggatcttcctaacatagtgtgagatg--ttgt-ctaacagTCATAATGGGAAGTTCAGCTACGGATATGCTAGTTCTCCCGGGAAAAGGTCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGAAGGAGAGMapped 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|192305900|gb|FG995786.1|FG995786EST: AGCGAGGTTCATGCTGCAGGTGATGCAATTGCGAGTGGTGGGGGGCTAAG TCACGATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATC
genomic: AGCGAGGTTCATGCTGCAGGTGATGCAATTGCGAGTGGTGGGGGGCTAAGgtaaatcctt ... gtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatgaagctgcatgagatgattgtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA
tttgttttgaattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctctggcatttcctttaaaaaaaaaaagaaagaaaaaaactaaacaatgaagctgcatgagatgattgtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - gcatttc
- - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacaca