Sequence
atgc intronic sequence ATGC exonic sequencegtatgaatactctaagaaaaacaaaaattatttatttgaatttccattctaaatggaattgaaataaactaattctcttctcttttagATTAACATGAAAGGCTTGGATGGTATACAAGGACCTACATATATTGGGACAGGATGTGTTTTTAGGAGGCAAGCACTCTATGGTTTTGATTCTCCAAGAA
Basic information
species | Glycine max |
transcript | GLYMA06G47420.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G47420.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 6
gtatgaatactctaagaaaaacaaaaattatttatttgaatttccattctaaatggaattgaaataaactaattctcttctcttttagATTAACATGAAAGGCTTGGATGGTATACAAGGACCTACATATATTGGGACAGGATGTGTTTTTAGGAGGCAAGCACTCTATGGTTTTGATTCTCCAAGAA
||| || | | | | | | || | | | | ||| | | | | | |||| | | || |||| ||||||||||||||||||||||| ||||| || | ||| |||| || |||||||| ||||| ||||| ||| | ||||||| |||| | || | ||
gtaagatttgccccatatttctgaga--tactctcctacacaagttatttaattttcttgcagtttatctaacatttgcttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA
upper sequence: GLYMA06G47420.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G082580_T01 (Zea mays), 3'ss of exon 8
----gtatgaatactctaagaaaaacaaaaattatttatttgaatttccattctaaatggaattgaaataaactaattctcttctcttttagATTAACATGAAAGGCTTGGATGGTATACAAGGACCTACATATATTGGGACAGGATGTGTTTTTAGGAGGCAAGCACTCTATGGTTTTGATTCTCCAAGAA
| | | | |||||| | | | || ||| | ||| | | | |||| || | | |||| ||||||||||| ||||||||||| ||||| || | ||| | || || ||||||||||| || |||| ||||| ||||||| |||| |||| | ||
gtaagattcagcttccctgttccaacaaacaccttaagctcttcgttttattgtccatgtcacatatgttttctaacacttgcatgatacagATCAACATGAAAGGTTTGGATGGTATTCAAGGGCCCATCTATGTGGGTACTGGATGTGTTTTCAGACGGCAGGCACTATATGGTTATGATGCTCCTAAAA
upper sequence: GLYMA06G47420.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 8
gtatgaatactctaagaaaaacaaaaattatttatttgaatttccattctaaatggaattgaaataaactaattctctt-ctcttttagATTAACATGAAAGGCTTGGATGGTATACAAGGACCTACATATATTGGGACAGGATGTGTTTTTAGGAGGCAAGCACTCTATGGTTTTGATTCTCCAAGAA
||| || | || | || | | || | | |||| || || || | | | || | | | | | |||| ||||||||||| ||||| ||||| |||||||| | ||| | || || ||||||||||| || |||| ||||| ||||||| |||| |||| | ||
gtaagattcaacttccctgttcgaacac-acaccttaagctcttcattttat-tgtcgatgtctcatattttttttgtaacacctgcagATCAACATGAAAGGTTTGGACGGTATTCAAGGACCCATTTATGTGGGTACTGGATGTGTTTTCAGACGGCAGGCACTGTATGGTTATGATGCTCCTAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgaatttccattctaaatggaattgaaataaactaattctcttctcttttagATTAACATGAAAGGCTTGGATGGTATACAAGGACCTACATATATTGGGACAGGATGTGTTTTTAGGAGGCAAGCACTCTATGGTTTTGATTCTCCAAGAA
aactaat putative branch site (score: 2)
ctaattctcttctctt CT-rich tract
aattgaaataaactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaatactctaagaaaaacaaaaattatttatttgaatttccattctaaatggaattgaaataaactaattctcttctcttttagATTAACATGAAAGGCTTGGATGGTATACAAGGACCTACATATATTGGGACAGGATGTGTTTTTAGGAGGCAAGCACTCTATGGTTTTGATTCTCCAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG