Sequence
atgc intronic sequence ATGC exonic sequencegttatttcttgcactttgttctgtttattgttcaccttgttcaatagttgaagcggtttgggctaaaaattttaattcacaagttctttctcttgctctgtgtgtgtgtattgtctttatttgtaattaatgtagttgtgtacagATTGAGATGCTTACACCAAAGGACTACATTGGTCCACTTATGGAACTGGCACAAGAAAGAAGAGGGCAGTTCAAAGAAATGAAATTTATTGCTGAAAATA
Basic information
species | Glycine max |
transcript | GLYMA06G16700.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 15
gttatttcttgcactttgttctgtttattgttcaccttgttcaatagttgaagcggtttgggctaaaaatttt--aattcacaagttctttctcttgctctgtgtgtgtgtattgtctttatttgtaattaatgtagttgtgtacagATTGAGATGCTTACACCAAAGGACTACATTGGTCCACTTATGGAACTGGCACAAGAAAGAAGAGGGCAGTTCAAAGAAATGAAATTTATTGCTGAAAATA
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--------------------------gttgtttcttctgtatacaggctttcaccgtccattacagtcatctttaagattgggagtgttgaattctgca-tgtatctgattctcttctttgatctctgc-attttttttttatttagATTGACATGCTTACACCAAAAGAGTATATTGGCCCAATAATGGAACTGGGTCAAGAGAGAAGAGGTGAATTCAAGGAAATGAACTTCATCACAGAAAATA
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 15
gttatttcttgcactttgttctgtttattgttcaccttgttcaatagttgaagcggtttgggctaaaaattttaattcacaagttctttctcttgctctgtgtgtgtgtattgtctttatttgtaattaatgtagttgtgtacagATTGAGATGCTTACACCAAAGGACTACATTGGTCCACTTATGGAACTGGCACAAGAAAGAAGAGGGCAGTTCAAAGAAATGAAATTTATTGCTGAAAATA
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-----------------gttgtatctgt-gtacatgatgttcacca-tcaatttgcagtga--cattattattgatctttgggagtagtgtcatgcacag-gcctggttattgtttttgat-gtcttcctttccctcctttgcagATTGAAATGCTTACACCAAAAGATTATATTGGTTCAATAATGGAGCTGACTCAAGACAGAAGAGGTGAATTCAAGGAAATGAACTTCATCACAGAAAGCA
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 15
gttatttcttgcactttgttctgtttattgttcaccttgttcaatagttgaagcggtttgggctaaaaattttaattcacaagttctttctcttgctctgtgtgtgtgtattgtctttatttgtaattaatgtagttgtgtacagATTGAGATGCTTACACCAAAGGACTACATTGGTCCACTTATGGAACTGGCACAAGAAAGAAGAGGGCAGTTCAAAGAAATGAAATTTATTGCTGAAAATA
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-------------------------------------------------gttgccttttctactggagatattg-ctgataagttcacacacc-acatttcgta---gaattacatttccttactgcaaaaccattt-tatacagATTGAACTGCTCACACCAAAAGACTATATTGGTGCGCTTATGGAGCTCGCTCAAGAGAGGAGAGGGGAGTTCAAAGAAATGAAATATATAGCTGAGAACA
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 15
gttatttcttgcactttgttctgtttattgttcaccttgttcaatagttgaagcggtttgggctaaaaattttaattcacaagttctttctcttgctctgtgtgtgtgtattgtctttatttgtaattaatgtagttgtgtacagATTGAGATGCTTACACCAAAGGACTACATTGGTCCACTTATGGAACTGGCACAAGAAAGAAGAGGGCAGTTCAAAGAAATGAAATTTATTGCTGAAAATA
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gttgttgcctgcatcta----tagatgttctcccatttagtcattttctgatata------tccagatatctt------taagttcttgtttcaaatcctaaagaaaaaaaggc---tatttgattttaaaacaat-atgtacagATTGAGATGCTCACTCCAAAAGACTATATCGGTCCTCTCATGGAATTGGCTCAAGACCGTAGAGGAGAGTTCAAAGAAATGAAATTTATCACTGAGAATAMapped 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|120494646|gb|EH222813.1|EH222813EST: TACTTCCTGAGCCTGGAAAAAGGAAATCAATTGAGGAGCCATTTGTTAAG ATTGAGATGCTTACACCAAAGGACTACATTGGTCCACTTATGGAACTGGCA
genomic: TACTTCCTGAGCCTGGAAAAAGGAAATCAATTGAGGAGCCATTTGTTAAGgttatttctt ... ttgtgtacagATTGAGATGCTTACACCAAAGGACTACATTGGTCCACTTATGGAACTGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgctctgtgtgtgtgtattgtctttatttgtaattaatgtagttgtgtacagATTGAGATGCTTACACCAAAGGACTACATTGGTCCACTTATGGAACTGGCACAAGAAAGAAGAGGGCAGTTCAAAGAAATGAAATTTATTGCTGAAAATA
aattaat putative branch site (score: 3)
tattgtctttatttgt 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
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gttatttcttgcactttgttctgtttattgttcaccttgttcaatagttgaagcggtttgggctaaaaattttaattcacaagttctttctcttgctctgtgtgtgtgtattgtctttatttgtaattaatgtagttgtgtacagATTGAGATGCTTACACCAAAGGACTACATTGGTCCACTTATGGAACTGGCACAAGAAAGAAGAGGGCAGTTCAAAGAAATGAAATTTATTGCTGAAAATA
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