Sequence
atgc intronic sequence ATGC exonic sequencegtacagctctttttcccctgcttttgtgtgtctgtgttgcttgcacttcccgcctcacatgcttctttagtttacttcttcccttttaaaagtttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
Basic information
species | Glycine max |
transcript | GLYMA16G33570.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 3
gtacagctctttttcccctgcttttgtgtgtctgtgttgcttgcacttcccgcctcacatgcttctttagtttacttcttcccttttaaaagtttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
| || | ||||| || ||| | | | | | || ||| || || || | | | ||| | |||| ||||||||||||||| |||| || || || || ||||||||||| ||||| || |||||||| || || || || ||||| || || |||||||||||
-----------------gtatttcatgctctctgtttt-tttgtatgaatctgtgtaggttcctcattaactttgtt-ttatgtgtcgatgtttt-----ttcagCATTGGACAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGC
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 3
gtacagctctttttcccctgcttttgtgtgtctgtgttgcttgcacttcccgcctcac-atgcttctttagtttacttcttcccttttaaaagtttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
|| || | ||| | | | | | | ||||| || || | |||| | | | |||| |||||||| |||||| | ||||| || || |||||||||||||| || || |||||||||||||| || |||| ||||| || ||||||||||||||
---------------------------------gtatttcatgcttcttttataggaagacccctgtaaagtttgtagctcccttgttaa---ccttgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 3
gtacagctctttttcccctgcttttgtgtgtctg-----tgttgcttgcacttcccgcctcacatgcttctttagtttacttcttcccttttaaaagtttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
|||| | | | || || || | || | || | | || | ||| | || ||| ||| || || |||||| |||||||||| |||||||||||||||||||| |||||||||||||| ||||| || |||||||||||||| ||||| | || ||||| || || || || ||||||||
gtactgtctctgcctctctctggctgggtttttggttcctttttccttcaatatatacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcagCATTGGACAGTGATGATCTACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGC
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S402_46V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------gtacagctctttttcccctgcttttgtgtgtctgtgttgcttgcacttcccgcctcacatgcttctttagtt--tacttcttcccttttaaa--agttta---aatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
| | | ||| | || || || || | | | | | ||| || | | || ||| |||| | || | ||| |||| ||||| ||||||||| | ||||| | || |||||||||||||| ||||||||||| ||||| | | ||| || ||||| |||||||| || ||
gtacagctcaaaacgctatttttagcacattgatatcctatgtactgcatgctgatgtttgatgcatgcagtgaagactccattgtgatggcggagtgtgttaattatcattgctgacctcttaatgcaattcatgaaatgcacagCATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCA--
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S88_45V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------gtacagctctttttcccctgcttttgtgtgtct-gtgttgcttgcact-tcccgcctcacatgcttctttagtt--tacttcttcccttttaaaagt--ttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
| | ||| | | || || | | ||| | | | | | || | |||| | | | | | | | | || | | | |||| |||||| ||||| || |||||| | ||||| | ||||| ||||||||||| ||||||||||| ||||| | | || || || ||||| | || ||||| ||
gtacagctcaaacaaagtttatatttacggaatcgagcaatggttatatttatagagatgaatttctatagagttgacgttgatgcttgtcatgtggactctattatgatgcttgtcatgtgttgattatcactgttgatatcatattggcattgataaaatgtgcagCATTGGATAGCGATGATTTGCTTTACTTGAAGGAACAAATGGAAGCTGAGGAGGATGCCGAGCGTTTGCGCCGGCGAACGGAAAAGAGAGCGTTTGCAGC
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ15111 (Selaginella moellendorffii), 3'ss of exon 3
gtacagctctttttcccctgcttttgtgtgtctgtgttgcttgcacttcccgcctcacatgcttctttagtttacttcttcccttttaaaagtttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
|||| | |||| | | ||||| | || || | | ||| | || || |||| || | | || || | |||||| | ||||| |||||||| || || ||||| || || |||||||||||||||||||| ||| |
gtactgttcttca--cttagtttttgaat-tccttgcatttctctaggaaaagctcgttttttttcttggttttctcacgttttcctgggaggttc--tttgcagCTCTTGACAGCGATGATCTTCTCTACCTCAAAGAACAGATGGAAGCCGAGGAGGATGCCGAGAGG-----------------------------------
upper sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ16082 (Selaginella moellendorffii), 3'ss of exon 3
gtacagctctttttcccctgcttttgtgtgtctgtgttgcttgcacttcccgcctcacatgcttctttagtttacttcttcccttttaaaagtttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
|||| | |||| | | ||||| | || || | | ||| | ||||| ||| | | | | | | | |||||| | ||||| |||||||| || || ||||| || || |||||||||||||||||||| ||| |
gtactgttcttca--cttagtttttgaat-tccttgcatttctctaggaaaagctcgtttttttcttggttttctcacgttttcctgggagggtc---tttgcagCTCTTGACAGCGATGATCTTCTCTACCTCAAAGAACAGATGGAAGCCGAGGAGGATGCCGAGAGG-----------------------------------Mapped 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|192298082|gb|FG991362.1|FG991362EST: GATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG CCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGG
genomic: GATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCGgtacagctct ... aaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgcctcacatgcttctttagtttacttcttcccttttaaaagtttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
gcctcac putative branch site (score: 3)
ttttaaaagtttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagctctttttcccctgcttttgtgtgtctgtgttgcttgcacttcccgcctcacatgcttctttagtttacttcttcccttttaaaagtttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC