Sequence
atgc intronic sequence ATGC exonic sequence...tgagtggcttgtactagtgtactctgtaagaatgtgttctagacattgaatattgtatatttctgatttcttattgtgatttggattgttgttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
Basic information
species | Glycine max |
transcript | GLYMA07G02170.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 5
tgagtggcttgtactagtgtactctgtaagaa---tgtgttctagacattgaatat-tgtatatttctgatttcttattgtgatttggattgttgttctt--aaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
| | |||||| | | || | |||| || | || | | | || | | | || | || || | | || | ||||||| || || ||||| ||||||||||| ||||| | ||| ||||| || ||||||||| |||| |||||||| |||||||||||||| ||||||| |
------tacagcattagtgtgttatatacaggctctctgtttatgattctcaagttatatggatgttagttaaagagctgaaacttcagttatcaattttgtacagGATGTTACGCTTCATGACCTTGATGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGACAGATGATGAAGCCACGGAAAACTG
upper sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
tgagtggcttgtactagtgtactctgtaagaatgtgttctagacattgaatattgtatatttctgatttcttattgtgatttggattgttgttctt--aaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
| || ||||| | || | || || | | || | | | | | | || | || ||| || | | ||||||| || || ||||| ||||| ||||| ||||| | ||| ||||| || ||||||||| |||| |||||||| || ||||||||||| | || || |
-tcatatgcagtgttagtgcattcaatctttctgc-ttatggctcttaagttatatggaagttaatgaatataggaaaacttctcctgtcatttatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG
upper sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 5
------tgagtggcttgtactagtgtactctgtaagaatgtgttctagacattgaatattgtatatttctgatttcttattgtgatttggattgttgttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
| | | |||||| | | | ||| | | | | | || | | || | | |||||| | | | || || || || ||||||| || || ||||| |||||||| || ||||| | || ||||| || ||||||||| |||| |||||||| |||||||||||||| |||| || |
taagaattaatt-cttgtatttgcat-ctcaacatggaggcctcctgtattct----atgctcttgttctgaagaggaaataacctcctcatcattttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTG
upper sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
tgagtggcttgtactagtgtactctgtaagaatgtgt-tctagacattgaatatt-gtatatttctgatttcttattgtgatttggattgtt-----gttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
| || || || || | || || ||| |||| || || | | | || |||| | ||| | | | | | ||||||| || || ||||| |||||||| || ||||| | || ||||| || ||||||||| |||| |||||||| ||||||||||| || | || || |
-----gatttttaataagaattaatgcttgtatttgcgtctcaacatggaggcttcatgtgctcttg--ttctgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
upper sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
--tgagtggcttgtac-tagtgtactctgtaagaatgtgttctagacattgaatattgtatatttctgatttcttattgtgatttggattgttgttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
||| | | | || || | | ||| | | || || |||| | |||| |||| ||| || | | |||||||||| || ||||| || |||||||| |||||||| |||||||| ||||||||||| |||| || |||||||||||||||||||| ||||||||||
ctaaagttacatctttataaggtgtggtttcagag-acacagtgggttccccatgttaattattcat--cttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
upper sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------tgagtg-gcttgtactagtgtactctgtaagaatgtgttc----tagacattgaatattgtatatttctgatttcttattgtgatttggat-tgttgttct-taaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
| | | ||| || |||||| | || | | | || | ||| ||||| ||| || | | |||||| |||| || |||| | | | ||||||| || || |||||||| |||||||| ||||| || |||||||| || |||||||| |||| | ||||| ||||||||||| ||| | || || |
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaa--tcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG
upper sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 5
tgagtggcttgtactagtgtactctgtaagaatgtgttctagacattgaatattgtatatttctgatttcttattgtgatttggattgttgttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
|| ||| || |||| | | || ||||| | | || | |||| || || || |||||||| |||||||| ||||| || |||||||| |||||||||||||| || | ||||| |||||||||||||| | || || |
-----------------------------------gtacta-actgtgaaga----aagggtccagtttctcttcacacagcaagtgtgggtgtatgtagGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTG
upper sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 5
tgagtggcttgtactagtgtactctgtaagaatgtgttctagacattgaatat--tgtatatttctgatttcttattgtgatttggattgttgttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
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------------------------------------------gtactaactgtgatgaaagggtccagtttctcttcacacagcaagtgggtgtattc--agGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGMapped 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|298197378|gb|HO044857.1|HO044857EST: GGAGATTGTTCAG GATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGA
genomic: GGAGATTGTTCAGgtatttaatt ... gttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGA
EST:
gi|18039885|gb|BM308179.1|BM308179EST: ATGTTCCACTTCCCAAGGGAGAGGTTCACNNNNNNNNGGAGATTGTTCAG GATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGA
genomic: ATGTTCCACTTCCCAAGGGAGAGGTTCACAAAAAAAAGGAGATTGTTCAGgtatttaatt ... gttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGA
EST:
gi|151398565|gb|EV268436.1|EV268436EST: ATGTTCCACTTCCCAAGGGAGAGGTTCACNNNNNNNNGGAGATTGTTCAG GATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGA
genomic: ATGTTCCACTTCCCAAGGGAGAGGTTCACAAAAAAAAGGAGATTGTTCAGgtatttaatt ... gttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaatattgtatatttctgatttcttattgtgatttggattgttgttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
ttctgat putative branch site (score: 3)
ttgttctt putative PPT
tattgtatatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgagtggcttgtactagtgtactctgtaagaatgtgttctagacattgaatattgtatatttctgatttcttattgtgatttggattgttgttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- -gtggctt
- - - - - - - - - - -ctctgta
- - - - - - - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg