Sequence
atgc intronic sequence ATGC exonic sequence...aagaaaattattatctgccacttggctgcatggttttatgataattaattttgtttatgatctgcatcctgatatttgtttgtcaattttatttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAG
Basic information
species | Glycine max |
transcript | GLYMA14G04410.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 10
aagaaaattattatctgccacttggctgcatggttttatgataattaattttgtttatgatctgcatcctgatatttgt-ttgtcaat---tttatttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAG
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-------gtatgctgcattaaccagttgtgacttttcagacgtgtcacttatcatttctgtttgctttttgttctatatattgacaatcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
upper sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g32360.1 (Oryza sativa), 3'ss of exon 10
----------------------------------aagaaaattattatctgccacttggctgcatggttttatgataattaattttgtttatgatctgcatcctgatatttgtttgtcaattttatttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAG
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gtatattttcttcttttagtttgcttactctgttgacataggaaatgcccgt-acctgcgtatttcctcagctgtcattgcatttcattactgagctgtaagttgacatgattttgcg--------ctgttcagAGGATATCAGCACAAGATGCACTTGATGCAGAGTATTTCTGGTCTGATCCCCTACCATGTGATCCTAAAAG
upper sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 10
------------------------------------------aagaaaattattatctgccacttggctgcatggttttatgataatta-attttgtttatgatctgcatcctgatatttgtttgtcaattttat---ttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAG
||||| ||| | | | | | | | || | || | | ||||| | ||| | | || |||| | | || | | ||||| || | || ||||||||||||||||| || ||||||||||| ||||| ||||| |||||||| || ||
gtatgctacattgcgtgaattactgtaagtttaatttgtttagtcaaaatggttagttcctatt---ccgtacttttctttggctgctgtgtgttgttcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG
upper sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 11
----aagaaaattattatctgccacttggctgcatggttttatgataattaattttgtttatgatctgcatcctgatatttgtttgtcaattttatttc-tacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAG
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tttgtttaaaggagttgattttagcatatatacacactt-----atatttctctttctccctctctaatatcctatgtccctttttttaaaattacaaaatgtagAGAATATCTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGMapped 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|193658856|gb|FK607287.1|FK607287EST: ATCATGCTCTGGAATTGTTGGAGAAGATGTTGACACTTGATCCGGCTCAG AGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCA
genomic: ATCATGCTCTGGAATTGTTGGAGAAGATGTTGACACTTGATCCGGCTCAGgtatcacttc ... atttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCA
EST:
gi|193650818|gb|FK595899.1|FK595899EST: ATCATGCTCTGGAATTGTTGGAGAAGATGTTGACACTTGATCCGGCTCAG AGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCA
genomic: ATCATGCTCTGGAATTGTTGGAGAAGATGTTGACACTTGATCCGGCTCAGgtatcacttc ... atttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattttgtttatgatctgcatcctgatatttgtttgtcaattttatttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAG
tcctgat putative branch site (score: 3)
ttttatttct putative PPT
atatttgtttgtcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaaaattattatctgccacttggctgcatggttttatgataattaattttgtttatgatctgcatcctgatatttgtttgtcaattttatttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
aagaaaa
- - - - - - - ctgccac
- - - - - - - - - - - - - -gcatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt