Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcagtgtatctttgataatctaatttttaattaatcccttaattaggatccattaattaattgtagtgatttgacggtaataccctccaaaaactgtgaataatggcatcctcataatctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGATTGGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT
Basic information
species | Glycine max |
transcript | GLYMA20G30230.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G25700.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtcagtgtatctttgataatctaatttttaattaatcccttaattaggatccattaattaattgtagtgatttgacggtaataccctccaaaaactgtgaataatggcatcctcataatctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGATTGGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT
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-----------------ttgtattttaatattggatacat------gtgatgacaaatgactttgttg-gctgcattaacacaaatgacct--ggtggct-----taattttaagctcgt--ccttgaaacagGGGTTAGGCATAACGGTGTTTGGAATCGCCTACATGTTTGTCCACGATGGTCTCGTGCACAAGCGTTTCCCTGTAGGTCCCATCGCCGACGTCCCTTACC
upper sequence: GLYMA20G30230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtcagtgtatctttgataatctaatttttaattaatcccttaattaggatccattaattaattgtagtgatttgacggtaataccctccaaaaactgtgaataatggcatcctcataatctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGATTGGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT
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------------------------------tccaaaca-tgaaagattgggtgtacttagactaatgaaaccactatacgagtactatctgtttcttgttttttgtgctgactggtttgtaatatc--accagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC
upper sequence: GLYMA20G30230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
----------gtgagtcagtgtatct-ttgataatctaatttttaattaatccct--taattaggat--ccattaattaattgtagtgatttgacggtaataccctccaaaaactgtgaataatggcatcctcataatctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGATTGGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT
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gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagttta--ccttcagcttacaaaatcagtgtt-tggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATTMapped 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|120492844|gb|EH221011.1|EH221011EST: CATACGGTTTTTTCCACAAGGGTCTGGTCCCTGGCCTCTGTTTTGGTGCA GGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGA
genomic: CATACGGTTTTTTCCACAAGGGTCTGGTCCCTGGCCTCTGTTTTGGTGCAgtgagtcagt ... ctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acggtaataccctccaaaaactgtgaataatggcatcctcataatctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGATTGGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT
atttgac putative branch site (score: 4)
tcttt putative PPT
ataatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcagtgtatctttgataatctaatttttaattaatcccttaattaggatccattaattaattgtagtgatttgacggtaataccctccaaaaactgtgaataatggcatcctcataatctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGATTGGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA