Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttcttacatttaaattttagcaatcttatgccttacttagtacctcattgcttgttaggatgattttgttgtactgtgatgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGCGACTTGATTTTTATGACAAGGGAGTTGCCCCTCGTAAGAACATAGATGT
Basic information
species | Glycine max |
transcript | GLYMA07G11560.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 6
gtttgtttcttacatttaaattttagcaatcttatgccttacttagtacctcattgcttgttaggatgattttgttgtactgtgatgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGCGACTTGATTTTTATGACAAGGGAGTTGCCCCTCGTAAGAACATAGATGT
||| ||| | || || || | | | | || ||| | | | ||||| | | | | || || |||| | ||| | |||||| | || || |||||||||||||||||||| | || || ||||||||||| ||||| |||||||| ||| | |||||
gttagttgcata-gttctgtttccaatttgtatgtccactagttactgctt--ttgctgaaagaacttgctgccatattttggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 6
----gtttgt-----ttcttacatttaaattttagcaatcttatgccttacttagtacctcattgcttgttaggatgattt-tgttgtactgtga--tgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGCGACTTGATTTTTATGACAAGGGAGTTGCCCCTCGTAAGAACATAGATGT
||| | ||| || | | || || || | ||||| | | | | | || | || ||| | |||||| | | |||| | || || |||||| | || | ||||||||||| |||||| |||| || || ||||||||||| ||||| |||||||| ||| | |||||
gttagttcgaggaagctctgtcaccggactgttttgtatgctaagt-ttactcattccaaaagcatctttttgattgttttgtactgtactcttgacttcagAGGCTAGCACCTCTGTCTTTGGGCAAAAGTTGCGTGAGCAAGTCGAGGAGAGACTGGAATTCTATGACAAGGGTGTTGCGCCTCGTAAAAACCTTGATGT
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G110233_T01 (Zea mays), 3'ss of exon 6
--------------gtttgtttcttacatttaaattttagcaatcttatgccttacttagta-cctcattgcttgttaggatgattttgttgtactgtgatgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGCGACTTGATTTTTATGACAAGGGAGTTGCCCCTCGTAAGAACATAGATGT
| | || | | | | || || | | | | | | | |||| |||| | | | || || || | | | |||| |||| || |||||| | || | || |||||||| |||||| |||| || || ||||||||||| ||||| |||||||| || | |||||
gttagttctaggaagctctgttaccggactgttttgtatgctattgtttcctcgatccaaaagcatcat--cttgattgttttatacctttatatttggtttcagAGGCTAGTACCTCTGTCTTTGGGCAAAAGTTGCGCGAGCAAGTCGAGGAGAGACTGGAATTCTATGACAAGGGTGTTGCGCCTCGTAAAAATCTTGATGT
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtttgtttcttacatttaaattttagcaatcttatgcctt--acttagtacctcattgcttgttaggatgattttgttgtactgtgatgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGCGACTTGATTTTTATGACAAGGGAGTTGCCCCTCGTAAGAACATAGATGT
| | | || | || | || | | | | | | || | || | | || || ||| ||||||| | | ||||| |||| || |||||||| | || ||||| ||||| ||||||| ||||||||||| || |||||||| |||||||| | |||||
gtaataatctagagaatgtcctgaataagagagaggtgtttgggagatgatgcgttgttattaactacaaaatcatggtggttgtgttatgcagATAACAGCACTACAGCTTTCGGTGAGAAACTAAGGGAACAAGTAGAGGAAAGACTTGACTTTTATGACAAAGGTGTTGCCCCACGTAAGAATGTTGATGT
upper sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 6
gtttgtttcttacatttaaattttagcaatcttatgccttact--tagtacctcattgcttgttaggatgattttgttgtactgtg-atgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGCGACTTGATTTTTATGACAAGGGAGTTGCCCCTCGTAAGAACATAGATGT
|| |||||| | || | | | || | || || | | | | || || || || | || | | || |||||| || || || ||||||||||||||||||||| ||||||||||||||||| || ||||||||||||||| |||| ||||| || ||||| |||||
gtaagtttctataaattcttatatggtcatttcatttctcatggatggcaactttttatctgataaatttgttgcacaatcttctgtgtgcagAGAGTAACACCACGGTTTTTGGGGAGAAACTCCGTGAACAAGTTGAGGAGCGACTCGAATTTTATGACAAGGGAATTGCACCTCGGAAAAACATTGATGTMapped 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|9985893|gb|BE660120.1|BE660120EST: CTATCTTGCTAACAAATGTTCAATTGCTTCACGGATTGACTGCTTTTCTG AAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGC
genomic: CTATCTTGCTAACAAATGTTCAATTGCTTCACGGATTGACTGCTTTTCTGgtttgtttct ... tgtgatgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGC
EST:
gi|192317143|gb|FK007882.1|FK007882EST: CTATCTTGCTAACAAATGTTCAATTGCTTCACGGATTGACTGCTTTTCTG AAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGC
genomic: CTATCTTGCTAACAAATGTTCAATTGCTTCACGGATTGACTGCTTTTCTGgtttgtttct ... tgtgatgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccttacttagtacctcattgcttgttaggatgattttgttgtactgtgatgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGCGACTTGATTTTTATGACAAGGGAGTTGCCCCTCGTAAGAACATAGATGT
gccttac putative branch site (score: 3)
atgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttcttacatttaaattttagcaatcttatgccttacttagtacctcattgcttgttaggatgattttgttgtactgtgatgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGCGACTTGATTTTTATGACAAGGGAGTTGCCCCTCGTAAGAACATAGATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC