Sequence
atgc intronic sequence ATGC exonic sequencegtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
Basic information
species | Glycine max |
transcript | GLYMA10G42250.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
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-------------------------------ggagcaaatagtgcatgattga-gccagttggg-----acatttactataca--tgttctgcag-----cctaaataa---tgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctga-atgtactttcctcttttaata---tgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
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------------------------------------------------ttgtttgaatgttacaag---gcatcagttatttgaaattagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G122135_T04 (Zea mays), 3'ss of exon 3
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttgga--acagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
| | ||||| || || || || | || || || | | | || | | | | | || || |||| ||||||||||||| || | ||||||||||| || || |||||||||||||| || |||||||||||||||||||||| || || || || || || |||||
-------------------------------------------------ctaatcattattgaatcattgagttagtgtttgcatatagtcatacacttttgggacatcattagggctatgtctaaaacgtcgtggtctttattttcagATCAAGATTCAGTGCGTTTGTTGGCTGTTGAAGGTTGTGCTGCTCTTGGTAAATTGTTGGAGCCACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGT
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctgaatgtactttc--ctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
||| ||| | ||| || || || || || || | | | | | | | || || | | | | || || | | ||||||||||||| || | |||||||||| || ||||||||||| ||||| || ||||||| ||||||||||| || ||||| || || || || |||||
-----------------------------------------------catgattgaat-ttgaatcattgggttagt-gtttgcatatagtcatacgcatttgggacatcattaggactatgtctaaacctgctggtctttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------gtaattgaatacatatttcttgttctttg-tagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgt-agaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttggaa-cagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
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gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttga-attaataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatattta-cattggttgtgtgattgtgttgtagaatctcctgaatgtactt-tcctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
|||| | || || || | || | || || || || || || ||| | | ||| | | | | |||||||||||||||| ||||| ||||| || ||||| |||||||||||||| || |||||||||| || |||||||| ||| || || || || |||||
---------------------------------------------------------------gtattgaacactgagcgtttatttactctacagcat-------atatatttgtcgaatttcatcttacgtttt--tttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
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---------------------------------ctgaagttaagcagaattacggttgtctacatctcagcttcagt-gtctttttatattataatat-tacagattttaagtatct-tattgacat------tgatat-----cagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGTMapped 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|193490519|gb|FK456386.1|FK456386EST: TCATTTGAAGGCTGATCTCATGTCAATTTTTGATGATCTTACTCAAGATG ATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGC
genomic: TCATTTGAAGGCTGATCTCATGTCAATTTTTGATGATCTTACTCAAGATGgtaattgaat ... cttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGC
EST:
gi|26057519|gb|CA800433.1|CA800433EST: TCATTTGAAGGCTGATCTCATGTCAATTTTTGATGATCTTACTCAAGATG ATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCA
genomic: TCATTTGAAGGCTGATCTCATGTCAATTTTTGATGATCTTACTCAAGATGgtaattgaat ... cttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
ttttaat putative branch site (score: 3)
ttttaatatgtgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG