Sequence
atgc intronic sequence ATGC exonic sequencegtatgcagttgcttgccatttcctttaatggttttaaaacaccaatgaaaagagatttgagtagtctcacaaaatatattcattatttttaccataaaatttttaaattggatctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACCAGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGATACTAATCTTAA
Basic information
species | Glycine max |
transcript | GLYMA05G09360.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 3
gtatgcagttgcttgccatttcctttaatggttttaaaacaccaatgaaaagagatttgagtagtctcacaaaatatattcattatttttaccataaaatttttaaattggatctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACCAGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGATACTAATCTTAA
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--------------------------------------------------------gtatgcaaatatgaatatttaacttactatatatatgcatgaatcgttgagt-aattctatcttttggctcgtttcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA
upper sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 3
gtatgcagttgcttgccatttcctttaatggttttaaaacaccaatgaaaagagatttgagtagtctcacaaaatatattcattatttttaccataaaatttttaaattggatctttgacttgctatgt--ttctttg-gtagTTGTTCGTACTCTTACCAGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGATACTAATCTTAA
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------------------------------------gtatgcacattagactttgggtgtttaatat-atgaattctgttcttttgatatgttgttaaactgatatctagagattttctgttgtaatgtggttttttgtatagTTGTTCGCACGCTTACTGGCCACAGATCAAATTGCATATCTGTGGACTTCCATCCATTTGGGGAGTTCTTTGCATCTGGCTCTCTGGACACAAATCTTAA
upper sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S9_241V6.1 (Physcomitrella patens), 3'ss of exon 3
--------gtatgcagttgcttgccatttcctttaat---ggttttaaaacaccaatgaaaa----------gagatttgagtagtctcacaaaatatattc---attatttttaccata----aaatttttaaattgg----atctttga-cttgct-atgtttctttg-------gtagTTGTTCGTACTCTTACCAGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGATACTAATCTTAA
|| | || || | | |||| | || ||| | | ||| | | |||| || || | || |||| || || | | || | || ||| || || || || ||| || | ||| | | | |||||| || |||||||| ||||| | || ||||||| |||||| || || |||||||| ||||||||||| || || || ||| ||||||| ||||| ||
gtaagcttgttagagctttctctctctctcctccggtccaagtattacatgattaatttgagtttctattccatggtttgtgtggtgtgcacgtattcattctagatcatggatgcgatgcttcgtacttctaatcaggcaaaattttagatcttactgacatttttatacctgggtgcagTTGTACGCACTCTTACAGGTCATCGATCAAATTGTATATCAGTAGATTTTCATCCTTTCGGAGAGTTCTTCGCGTCGGGATCTCTAGATACAAATCTCAA
upper sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S101_210V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------gtatg-cagttgcttgccatttcctttaatggtt-ttaaaacaccaatgaaaagagatttgagtagtctcac----aaaatatattcattatttttaccataaaatttttaaattggatctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACCAGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGATACTAATCTTAA
| || ||||||||| ||| ||| | | || | | || | | ||| || | | || |||| | || || || | ||| |||| | | | |||||| || |||||||| |||| | || ||||| | ||| || || ||||||||||| |||||||||||||| || || ||||| ||||| ||||| ||
gtaagcttgcgaatgtcatctcctaggatatcagttgctttttattaacttgcgttcctattggatggattgtataacataactcattctatcttacttttgacggagatccattgctcttttgatctgatgag-gtgctcgattactgacccgtataagcgcgagtgcagTTGTACGCACTCTTACAGGTCACCGATCAAATTGCATATCTGTAGATTTCCATCCTTTCGGAGAGTTCTTTGCGTCGGGATCTTTGGATACAAATCTCAAMapped 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|193724235|gb|FK662283.1|FK662283EST: TGGAGCTGCGAGTGGTACCATCAAACTTTGGGACTTAGAAGAGGCAAAGN TTGTTCGTACTCTTACCAGTC
genomic: TGGAGCTGCGAGTGGTACCATCAAACTTTGGGACTTAGAAGAGGCAAAGAgtatgcagtt ... tctttggtagTTGTTCGTACTCTTACCAGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttaccataaaatttttaaattggatctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACCAGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGATACTAATCTTAA
ctttgac putative branch site (score: 4)
tgtttcttt putative PPT
ataaaatttttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcagttgcttgccatttcctttaatggttttaaaacaccaatgaaaagagatttgagtagtctcacaaaatatattcattatttttaccataaaatttttaaattggatctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACCAGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGATACTAATCTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA