Sequence
atgc intronic sequence ATGC exonic sequence...taatggatttatttaagtaagccttccattctaaatcacattaagcgctagttgtcctattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG
Basic information
species | Glycine max |
transcript | GLYMA07G18160.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
---taatggattta--tttaagtaagccttccattctaaatcacattaagcgctagttgtcctattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG
|| | || | || || || | | | | | | ||| ||| || | | | || | | ||| || | | | | | ||||| | ||||||||||||||||||| ||||| || |||||||| ||||||||||| |||||| | ||||| ||||| ||||| || || ||||| || ||||| |||
ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttct---ttttacaactttcctattcctgtttggt--agATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 4
taatggatttatttaagtaagccttccattctaaatcacattaagcgctagt-tgtcctattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG
| | || |||| ||| | | |||| | | | | || | || | ||| | | | || | | || |||||||||||||||| || |||||||| |||||||| ||||||||||| |||||| ||||||||||||| ||||| || || ||||| || ||||| |||
-ttcgcctgccatttagtactcctgtaacttgtcatcatgctgtcatcaattctgcattttttctttcattctgctaactataccttattctttttggtagATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGGCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG
upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 2
taatggatttat--ttaagtaagccttccattctaaatcacatt--aagcgctagttgtcctattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG
| | | || |||| || | || || | || || | | ||||| | | | | | | || || | |||||||||||||||| || |||||||| |||||||| ||||||||||| |||||| |||| |||||||| ||||| || || ||||| || ||||| |||
--gctcacctgtcatttagtactgctataacctgtaaccatgctgtaatcgttctgcaattttttctttcattctgctaactataccttttctttttggt--agATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGTCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG
upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
taatggatttatttaagtaagccttccattctaaatcacattaagcgctagttgtcctattcttgatatttaaccattgttt--tctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG
||| || || ||| || | | || | || | | | | || | | | | || |||| | | || ||||||||||||||||||||||||| ||||| |||||||||||||| | |||| || |||| |||||||||||||||||||| || || ||||| |||
-gcaagatataattctgtat-ccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG
upper sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
-taatggatttatttaagtaagccttccattctaaatcacattaagcgctagttgtcctattcttgatatttaaccattgttttctcact----gttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG
|| | | | | | ||| || || || ||| | | | | | ||| | |||| || | ||| || | |||| |||||||||||||| || ||||||||||| ||| | ||||| ||||||||||||||||| ||||||||||| |||||||||||||| || || ||||||||||||
gagataggataaaattggaaag--ttatgttttagatc---tggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAGMapped 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|21678030|gb|BQ630381.1|BQ630381EST: CAGAATATGTTGTTGCACTTGCTACTATTGTTGGATCTGTGCTTTTTGCT ATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCA
genomic: CAGAATATGTTGTTGCACTTGCTACTATTGTTGGATCTGTGCTTTTTGCTgtaagctcat ... ttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCA
EST:
gi|254348008|gb|GR854257.1|GR854257EST: CAGAATATGTTGTTGCACTTGCTACTATTGTTGGATCTGTGCTTTTTGCT ATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCA
genomic: CAGAATATGTTGTTGCACTTGCTACTATTGTTGGATCTGTGCTTTTTGCTgtaagctcat ... ttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgctagttgtcctattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG
ttctcac putative branch site (score: 2)
ttttctcactgttc CT-rich tract
tattcttgatatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatggatttatttaagtaagccttccattctaaatcacattaagcgctagttgtcctattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - -ccttcca
- - - - - - - - - - - - - - - - -aatcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcactg