Sequence
atgc intronic sequence ATGC exonic sequencegtcagttctgtcagagtgtgtgattcttgtcactgatgattgtgaataccttatattttgcaacctgtttttgtttgctctcatttatttctgccttttgaattttcttctgtgcctaatttgtggtttttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT
Basic information
species | Glycine max |
transcript | GLYMA13G28720.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 10
gtcagttctgtcagagtgtgtgattcttgtcactgatgattgtgaataccttatattttgcaacctgtttttgtttgct-ctcatttatttctgccttttgaatttt---cttctgtgcctaatttgtggtttttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT
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-----------------------------------------gtccacatttt-tatcttgtgttttttttatatataatgcttttctgcctatgttttatgttttcataacatttgtgtatacacaactgtgtatc-ctgcagATGACTAGGCTCTTGGACATCTTGGAAGATTATCTGATGTACAAGGGGTATCAATATTGCCGAATTGATGGGAATACTGGTGGTGAAGATCGTGATGCTT
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 10
gtcagttctgtcagagtgtgtgattcttgtcactgatgattgtgaataccttat-attttgcaacctgtttttgtttgctctcatttatttctgccttttgaattttcttctgtgcctaatttgtggtttttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT
|||| ||| | | ||| || | | |||| || | |||| || ||| | || | || | | | | | || |||||||| ||||| | || ||| | ||||||||| | ||| | || ||||| |||||||| || ||||||||||||||||| || ||||| ||||| |
------------------------------------tgatc-tgagttctctattgttcctaagcatgttaacgtcacacataatttggttt---cttcaaatcttgtgtttgactttgacatttatgtccattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 10
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 10
gtcagttctgtcagagtgtgtgattcttgtcactgatgattgtgaataccttatattttgcaacc-tgtttttgtttgctctcatttatttctgccttttgaattttcttctgtgcct--aatttgtggtttttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT
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------------------------------------tgatc-tgagttctctatggttcctaagcatgttaacgt-----cacacataatttggtttcttcaaatctcgtgtttgactttgacatttatgtccattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
--------------gtcagttctgtcagagtgtgtgattcttgtcactgatgattgt----gaataccttatat---tttgcaacctgtttttgtttgc------tctcattta--tttctgccttttgaattttcttctgtgcctaatttgtggtttttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT
|| | || || | ||| | | | || ||| ||| | | | | || | || ||| | |||||| | | | | | || || | ||||| | | | | |||||||| ||||| | || || | ||||||||| | ||| | | |||||||| ||||| || |||||||||||||| ||||| || ||||| ||||| |
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgac--atagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
gtcagttctgtcagagtgtgtgattcttgtcactgatgattgtgaataccttatattttgcaacctgtttttgtttgctctcatttatttctgccttttgaattttcttctgtgcctaatttgtggtttttctcc-ccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT
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-----------------------------gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTTMapped 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|254345542|gb|GR851704.1|GR851704EST: TACTTCCTAAATTGAAAGAGCGCGATTCTAGGGTCCTTATATTTTCACAG ATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATAT
genomic: TACTTCCTAAATTGAAAGAGCGCGATTCTAGGGTCCTTATATTTTCACAGgtcagttctg ... ttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATAT
EST:
gi|208167495|gb|GD965147.1|GD965147EST: TACTTCCTAAATTGAAAGAGCGCGATTCTAGGGTCCTTATATTTTCACAG ATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATAT
genomic: TACTTCCTAAATTGAAAGAGCGCGATTCTAGGGTCCTTATATTTTCACAGgtcagttctg ... ttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttctgccttttgaattttcttctgtgcctaatttgtggtttttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT
gcctaat putative branch site (score: 3)
tggtttttctcccc putative PPT
ttttgaattttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttctgtcagagtgtgtgattcttgtcactgatgattgtgaataccttatattttgcaacctgtttttgtttgctctcatttatttctgccttttgaattttcttctgtgcctaatttgtggtttttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG