Sequence
atgc intronic sequence ATGC exonic sequence...gatgtcaatttaaagattaaaaaatatatctttggagtttctgatttatttactccgatttgtttcttagtggtcgatctcatttgttgggatattgcagAAGTTATTACCGGTGCACCCACAACAACTGTAGGGTGAAGAAGAGGGTTGAACGACTATCAGAGGATTGTCGTATGGTGATAACCACCTATGAAGGTAGA
Basic information
species | Glycine max |
transcript | GLYMA09G37930.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G37930.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g46060.1 (Oryza sativa), 3'ss of exon 3
gatgtcaatttaaagattaaaaaatatatctttggagtttctgatttatttactccgatttgtttct---tagtggtcg-atctcatttgt-tgggatattgcagAAGTTATTACCGGTGCACCCACAACAACTGTAGGGTGAAGAAGAGGGTTGAACGACTATCAGAGGATTGTCGTATGGTGATAACCACCTATGAAGGTAGA
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----tgaatcgctctctctctcagcttg-ctgaccagtccgtacttaatctgtgttggtgtgcgcgtgtgtactgtttgtgtgcaaattgtgcatgcaaatgcagGAGCTACTACAGGTGCACCCACAACAACTGCCGCGTGAAGAAGCGGGTGGAGCGGCTGTCGGAGGATTGCCGCATGGTGATCACCACCTACGAGGGCCGC
upper sequence: GLYMA09G37930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G123387_T01 (Zea mays), 3'ss of exon 3
gatgtcaatttaaagattaaaaaatatatctttggagtttctgatttatttactccgatttgtttcttagtggtcgat---ctcatttgttgggatattgcagAAGTTATTACCGGTGCACCCACAACAACTGTAGGGTGAAGAAGAGGGTTGAACGACTATCAGAGGATTGTCGTATGGTGATAACCACCTATGAAGGTAGA
| | || | | || | | | |||| | || | |||||| | | |||| | | | | | | | || || | | ||| || || |||||||||||||||| |||||| | ||||||||| | || || | ||||| ||||| || || |||||||| ||||||||||| ||| |
--tattgatattatattttcagttcaaagctttaaacttcataatttatg-gtttcagtttgctggtgaacctttagttaccactttccatgcgtccatccagGAGCTACTACCGGTGCACCCACAGCAACTGCCGCGTGAAGAAGCGAGTGGAGAGGCTATCGGAGGACTGCCGCATGGTGATGACCACCTATGAGGGTCGC
upper sequence: GLYMA09G37930.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G44745.1 (Arabidopsis thaliana), 3'ss of exon 3
gatgtcaatttaaagattaaaaaatatatctttggagtttctgatttatttactccgatttgtttct-tagtggtcgatctcatttgttgggatatt---gcagAAGTTATTACCGGTGCACCCACAACAACTGTAGGGTGAAGAAGAGGGTTGAACGACTATCAGAGGATTGTCGTATGGTGATAACCACCTATGAAGGTAGA
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-ttcccaact---atttttgaacatattcacacgtttttaatggttaattgaatttaattattatgtctaatgatgtgtattaatgaatgaaacatataaacagGAGTTATTACAGATGCACACACAACAACTGTAGGGTGAAAAAGAGAGTGGAGCGACTATCGGAAGATTGTAGAATGGTGATTACTACTTACGAAGGTCGTMapped 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|151403781|gb|EV273591.1|EV273591EST: AAATGGAGGAAATATGGCCAGAAAGTTGTCAAGAATAGCCTTCATCCAAG AAGTTATTACCGGTGCACCCACAACAACTGTAGGGTGAAGAAGAGGGTTGA
genomic: AAATGGAGGAAATATGGCCAGAAAGTTGTCAAGAATAGCCTTCATCCAAGgtaatattca ... gatattgcagAAGTTATTACCGGTGCACCCACAACAACTGTAGGGTGAAGAAGAGGGTTGA
EST:
gi|13312038|gb|BG405698.1|BG405698EST: AAATGGAGGAAATATGGCCAGAAAGTTGTC-ATAATAGCCTTCATCCAAG AAGTTATTACCGGTGCACCCACAACAACTGTAGGGTGAAGAAGAGGGTTGA
genomic: AAATGGAGGAAATATGGCCAGAAAGTTGTCAAGAATAGCCTTCATCCAAGgtaatattca ... gatattgcagAAGTTATTACCGGTGCACCCACAACAACTGTAGGGTGAAGAAGAGGGTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttactccgatttgtttcttagtggtcgatctcatttgttgggatattgcagAAGTTATTACCGGTGCACCCACAACAACTGTAGGGTGAAGAAGAGGGTTGAACGACTATCAGAGGATTGTCGTATGGTGATAACCACCTATGAAGGTAGA
atttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgtcaatttaaagattaaaaaatatatctttggagtttctgatttatttactccgatttgtttcttagtggtcgatctcatttgttgggatattgcagAAGTTATTACCGGTGCACCCACAACAACTGTAGGGTGAAGAAGAGGGTTGAACGACTATCAGAGGATTGTCGTATGGTGATAACCACCTATGAAGGTAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttgg