Sequence
atgc intronic sequence ATGC exonic sequence...atagactaatagactaactgacaggctgtccttattattgactctcattataaaccctaacttaccttttattcacactttgtttatatctatgtaacagGAGTGGGCAATATGTATGGGAGGACCATCGCCCTAGATCTGGTGTATGGAAGGGATCTAGTGGTGGAGACATTATCTGCTTCAGTGGATGCGATGATCAT
Basic information
species | Glycine max |
transcript | GLYMA01G10880.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G10880.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G035928_T01 (Zea mays), 3'ss of exon 2
atagactaatagactaactgacaggc---tgtccttattattgactctcattataaaccctaacttaccttttattcacactttgtttatatctatgtaacagGAGTGGGCAATATGTATGGGAGGACCATCGCCCTAGATCTGGTGTATGGAAGGGATCTAGTGGTGGAGACATTATCTGCTTCAGTGGATGCGATGATCAT
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-tatccttaggta-tggctgataatcatatacatctataagagattctagttatgatagacatctcttcagctaaggattctt-atctatattgatattacagGAGTGGGCAATATGTATGGGAAGATCACCGACCGCGATCTGGTGTCTGGAAAGGCACTAGTGGTGGGGAAGCTATTTCCTTTAGTGGTTGTGATGATGAT
upper sequence: GLYMA01G10880.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G155422_T01 (Zea mays), 3'ss of exon 2
atagactaa-tagactaactgacaggctgtccttattattgactctcattataaaccctaacttaccttttattcacactttgtttatatctatgtaacagGAGTGGGCAATATGTATGGGAGGACCATCGCCCTAGATCTGGTGTATGGAAGGGATCTAGTGGTGGAGACATTATCTGCTTCAGTGGATGCGATGATCAT
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ttgtattaggtatggctcataatcatatacatctataagagattctagttatgatagacatctcttcagctaag-gccttttatctaaattgatattacagGAGTGGGCAATATGTATGGGAAGATCACCGACCACCATCTGGTGTCTGGAAAGGCACTAGTGGTGGGGAGGCTATTTCATTTAGTGGTTGTGATGATGAT
upper sequence: GLYMA01G10880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0013g00210.t01 (Vitis vinifera), 3'ss of exon 2
-----------atagactaatagactaactgacaggctgtccttattattgactctcattataaaccctaacttaccttttattcacactttgtttatatctatgtaacagGAGTGGGCAATATGTATGGGAGGACCATCGCCCTAGATCTGGTGTATGGAAGGGATCTAGTGGTGGAGACATTATCTGCTTCAGTGGATGCGATGATCAT
||||| |||||| | | | ||| ||| | || || | | | | ||| | |||| | | || ||||| || || || || || ||||||||||| |||||||||||| |||| ||||||||||| || | |||||||| || | || | || ||||| || |||||||||
tgttttaaaaaatagaa-aatagaaatgcatcaaaatggatactatcatt--ttttccttgtccattccaccttgc---ttatggatatttcctttatggacat-----agAAGCGGACACTATGTATGGGAAGACCATCGCCCTCGATCAGGTGTATGGAAAGGGACAAGTGGTGGGGAGGTCATTTCTTTTAGTGGTTGTGATGATCAT
upper sequence: GLYMA01G10880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0021g00990.t01 (Vitis vinifera), 3'ss of exon 4
------atagactaatagactaactgacaggctgtccttattattgactctcattataaaccctaacttaccttttattcacactttgtttatat---ctatgtaacagGAGTGGGCAATATGTATGGGAGGACCATCGCCCTAGATCTGGTGTATGGAAGGGATCTAGTGGTGGAGACATTATCTGCTTCAGTGGATGCGATGATCAT
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tttactacgggcttagtaactt-ttgaccag--gtccaaattgtt---cctcaccccaaa---tagttttcctgtcactactgttttacatatttttcctttggaacagGAGTGGACAGTATATATGGGAGGACCATCGCCCTCAATCAGGTGTATGGAAAGGAACAAATGGTGGAGAAGTCATTTCCTTTAGTGGTTGTGATGATGATMapped 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|151404758|gb|EV274572.1|EV274572EST: TGCCATAGTGGCACTGTTCTAGATTTGCCATTTCTTTGCAGAATGAACAG GAGTGGGCAATATGTATGGGAGGACCATCGCCCTAGATCTGGTGTATGGAA
genomic: TGCCATAGTGGCACTGTTCTAGATTTGCCATTTCTTTGCAGAATGAACAGgttaccttct ... tatgtaacagGAGTGGGCAATATGTATGGGAGGACCATCGCCCTAGATCTGGTGTATGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattataaaccctaacttaccttttattcacactttgtttatatctatgtaacagGAGTGGGCAATATGTATGGGAGGACCATCGCCCTAGATCTGGTGTATGGAAGGGATCTAGTGGTGGAGACATTATCTGCTTCAGTGGATGCGATGATCAT
aacttac putative branch site (score: 2)
tttgtttatatctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagactaatagactaactgacaggctgtccttattattgactctcattataaaccctaacttaccttttattcacactttgtttatatctatgtaacagGAGTGGGCAATATGTATGGGAGGACCATCGCCCTAGATCTGGTGTATGGAAGGGATCTAGTGGTGGAGACATTATCTGCTTCAGTGGATGCGATGATCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - -ctaactg
- - - - - - - - - - - aggctgt