Sequence
atgc intronic sequence ATGC exonic sequence...gatgactggtctgtttttgaaaaccttgtgttcaagttcagtattttttagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCTTATCGTG
Basic information
species | Glycine max |
transcript | GLYMA09G39770.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 11
gatgactggtctgtttttgaaaaccttgtgttcaagttcagtattttttagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCTTATCGTG
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----gtatgtatatttttctta---ttatatcccagccttgcatagttgcattccttgaatctactttg-catgttgttttactctctcattt----cagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 10
gatgactggtctgtttttgaaaaccttgtgttcaagt-tcagtattttttagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCTTATCGTG
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--------gtttgtattctatatgcttattttctagcctttgcactgcttaaaagttaaaactacttttgattt--tatggtactactattc-----acagGCTGGGTTATCGATGGCACTTGGAGCTTTTTTGGCTGGTCTGTTACTAGCAGAAACAGAGTTCTCCTTACAGGTTGAGTCAGATATAGCTCCTTATCGTG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 14
lower sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 10
gatgactggtctgtttttgaaaaccttgtgttcaagttcagtattttt-tagttcattaaattgatcttgacttgtttttgtt------ttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCTTATCGTG
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--------gtatgttcttgattttcc-gtgttggtgcttggtattctcgtaatt--ttgctttgtcttttgtttcgttaagataaattgtttctttctttaaattagGCGGGACTTTCCATGGCATTAGGAGCGTTTTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 11
gatgactggtctgtttttgaaaaccttgtgttcaagttcagtattttttagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCTTATCGTG
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--------gtatgaccgtga---ccttgt--tggcattgagtagtttactgacatgccagtacttcccgtctgctaatttttccagtttctataaatcagGCTGGACTTTCCATGGCATTAGGAGCGTTTTTGGCTGGTCTACTCCTTGCAGAGACAGAATTTTCGTTGCAAGTAGAATCAGATATTGCTCCATATCGTG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 9
gatgactggtctgtttttgaaaaccttgt-gttcaagttcagtattttttagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCTTATCGTG
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--gtattggatgcttttcataattattattattcttttcttataccaatcaagttgtgtctcccttttttccttaagaaaaaatcatttttcttgaa-cagGCAGGCCTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTGCTTCTTGCAGAAACTGAATTTTCCTTACAGGTTGAATCAGATATTGCTCCATATCGTGMapped 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|16996864|gb|BM086236.1|BM086236EST: CAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAGCCAGA GCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCA
genomic: CAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAGCCAGAgtatgtcata ... cttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCTTATCGTG
tcttgac putative branch site (score: 3)
cttgtttttgttttcc CT-rich tract
ttcattaaattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgactggtctgtttttgaaaaccttgtgttcaagttcagtattttttagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCTTATCGTG
-atgactg
- - - - gtctgtt
- - - - - - - - - gaaaacc
- - - - - - - - - - - - - tgtgttc