Sequence
atgc intronic sequence ATGC exonic sequencegtatgaattggctatttttgttgtcttgataattcctaaatatgttgaaaatcattgccctttattgtgtgagttcagGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC
Basic information
species | Glycine max |
transcript | GLYMA09G41380.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g55060.1 (Oryza sativa), 3'ss of exon 4
-----------gtatgaattggctatttttgttgtcttgataattcctaaatatgttgaaaatcattgccct------ttattgtgtga--gttcagGAGGTGGGTTTA---ATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC
| | | | | |||||| || || | | | | | | | || | ||| | | ||| || | |||||| | ||| ||||||| ||||| || ||||||||||||| || ||| ||||||||||||||||| || || || || ||||| ||||||||
gtaactcttttttttttccttgtgaggattgttggctatcaaacactcacaggaggttgttgttgtcaccttgttcgattaatatatgacaatttcgtagGTGGAGGCATCCGGAATATTCTAGTAATTGGTGCCGATGCTCTTTCACAATTTGTGGATTGGACAGACAGAGGTACATGCATCCTCTTTGGTGATGCTGC
upper sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G022563_T01 (Zea mays), 3'ss of exon 4
-----gtatgaattggctatttttgttgtc-ttgataattcctaaat---atgttga-aaatca-ttgccctttat-tgtgtgagttc--agGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC
| ||| ||||| ||| || ||| | | || || | || | | ||| ||| ||| || | || ||| || || ||| | ||||| |||| ||||| || |||||||||||| ||| || ||||||||||||||||| || || ||||||||||| ||||||||
gtaattcagttattaaatatttatgtggttgttggtgaatcatactctcaaaattaatatgtcacttgaataatatatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC
upper sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G003190_T01 (Zea mays), 3'ss of exon 4
---------gtatgaattggctatttttgttgtcttga-taattcctaaatatgttgaaaatcat-tgccctttattgtgtg-agttcagGAGGTGGG---TTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC
||| || | ||| | | | ||| | | | | | | | | || ||| || | ||| | |||||| ||| | ||| | ||||| |||| || |||||||||||| |||||| ||||||||||||||||| || || || |||||||| ||||||||
gtaattaaaatattaaatatttatctggttgatggtgaatggcttccacaaaaacaatatgccgcatgaataatataatgcatacttctgtagGTGGAGGTTTTCAGAATATCCTAGTAGTTGGTGCTGATGCTCTTTCAAAATATGTGGATTGGACAGACAGAGGTACATGCATCCTTTTTGGTGATGCTGC
upper sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G111677_T01 (Zea mays), 3'ss of exon 2
-----gtatgaattggctatttttgttgtc-ttgataattcctaaatatgttgaaaatcat-tgcccttt----attgtgtgagttc------agGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC-------------------
| ||| ||||| ||| || ||| | | || | | || ||| | || |||| || | | | || | | ||| || || ||| | ||||| |||| |||| || |||||||||||| || || ||||||||||||||||| || || ||||||||||| ||||||||
gtaattcagttattaaatatttatgtagttgttggtgaatcacac---tcttaaaattaatatgccacttgaataatatatgcatacttttgtaggcggaggtttttagaatgtcttagtagttggtgcagatgctctttcaaactacgtggattggacagACAGAGGTACATGCATTCTTTTTGGTGATGCTGCTGGTGCTGTGTTGGTACAG
upper sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0154g00140.t01 (Vitis vinifera), 3'ss of exon 4
gta-tgaattggctatttttgttgtcttgataattcctaaat-------atgttgaaaatcattgcccttta-ttgtgtgagtt-cagGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC
||| | || | | || | ||| | | | ||| | || | | | | || || || ||||| | || |||| ||||||||| |||||||||| || ||||| || ||||||||||| || |||||||||||||| || ||||||||||||||||| ||||||||||||||
gtaactagtttgtttgcttggctgtagtaaggttccctttctttcttccgtggttcatacaactgaactctacttgtgcaaattgcagGCGGTGGGTTTCATAATGTTCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGC
upper sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0233g00060.t01 (Vitis vinifera), 3'ss of exon 4
gta-tgaattggctatttttgttgtcttgataattcctaaat-------atgttgaaaatcattgcccttta-ttgtgtgagtt-cagGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC
||| | || | | || | ||| | | | ||| | ||| | | | | || || || ||||| | || |||||||||||||| |||||||||| || ||||| || ||||||||||| || |||||||||||||| || ||||||||||||||||| ||||||||||||||
gtaactagtttgtttgcttggctgtagtaaggttccctttcttgcttccatggttcatacaactgaactctacttgtgcaaattgcagGAGGTGGGTTTCATAATGTTCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGC
upper sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S119_22V6.2 (Physcomitrella patens), 3'ss of exon 6
----------------------gtatgaattggctatttttgttgtcttgataattcctaaatat--gttgaaaatcattgccctttattgtgtgagttcagGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC
|| | || | | | || ||| | || | | || | | | | | | ||||| | ||||||| || | || ||||| || || | || ||||||||||| || ||||| || |||||||| ||||||||||| |||||||| ||||| ||||| |
gggaaactaagtccactgaaaggtgcacttaattcatcctatctacttagagaatcacatgatgttggctgtctaaaactaacttcgaaagtgtg--tgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC
upper sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S87_63V6.1 (Physcomitrella patens), 3'ss of exon 6
------gtatgaattggctatttttgttgtcttgataattcctaaatatgttgaaaatcatt--------gccctttattgt-----------gtgagttcagGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC
|| |||||| | | ||||| | ||| | |||| || |||||| || ||| ||| | || || ||||||| || | | | ||||| || || | || || || ||||| ||| |||| || |||||||| ||||||||||| |||||||| ||||| ||||| |
tcgcatgttgtaattgg-tgtctttgtaagcagtttaacacttaaa-at-ttgaaagccaactgatagcggccacttaaagctaagattgaaggtacgtgcagGAGGAGGATATCAAAATGTGCTCGTGGTGGGTGCTGACGCTCTCTCAAGATACGTGGATTGGACGGACAGAGGGACGTGTATTCTATTTGGCGATGCCTCMapped 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|15203045|gb|BI425813.1|BI425813EST: ATGTAGTGGATTTGTGTTGGGTTTAATATCAGCTGCTTGCCACATTAGGG GAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGAT
genomic: ATGTAGTGGATTTGTGTTGGGTTTAATATCAGCTGCTTGCCACATTAGGGgtatgaattg ... gtgagttcagGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGAT
EST:
gi|192330256|gb|FK020556.1|FK020556EST: ATGTAGTGGATTTGTGTTGGGTTTAATATCAGCTGCTTGCCACATTAGGG GAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGAT
genomic: ATGTAGTGGATTTGTGTTGGGTTTAATATCAGCTGCTTGCCACATTAGGGgtatgaattg ... gtgagttcagGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgataattcctaaatatgttgaaaatcattgccctttattgtgtgagttcagGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC
tcctaaa putative branch site (score: 2)
taaatatgttgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaattggctatttttgttgtcttgataattcctaaatatgttgaaaatcattgccctttattgtgtgagttcagGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC