Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttgattttcattattgtgtccttcactatttcttttcttatggatatcaatttattttctcattagatagcaataaaaacttgaatactcatgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
Basic information
species | Glycine max |
transcript | GLYMA11G20130.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G20130.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g57400.2 (Oryza sativa), 3'ss of exon 4
gtatgtttgattttcattat-tgtgtccttca-ctatttcttttcttatggatatcaatttattttctcattagatagcaataaaaacttgaatactcatgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
|| ||| | | ||| | | | | ||| || || | | | || ||| | | | | |||| | | || || || ||||||||||| ||||||||||| ||||| || |||||||||||| || ||||| | |||||||| |||||| |||| |||| ||||||||||||||||| |
gtgcgttgcgtactagttagatatttgcatcaattacttatactttgttgcatactagagaactg-------atgtagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA
upper sequence: GLYMA11G20130.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g39870.2 (Oryza sativa), 3'ss of exon 1
------------------------------------------------------------------------------gtatgtttgattttcattattgtgtccttcactatttcttttcttatggatatcaattt--attt--tctcattagatagcaataaaaacttgaatactcatgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
|| || ||| | || | || | ||| | ||| || |||| || || | | || | || ||| | ||||||||||| |||| |||||||||||| || ||||| |||||||| |||| | |||||| || ||| || || ||||| |||||||||||||| |
gtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatattt---cagATGGGGCTAATGAGGAAACATCCTTCTATAATACCTTTTATGATCTACATATCCGATGAGGGCAAGCACACCGAGAGGTTTGCCGTACGTGCAAAGTACA
upper sequence: GLYMA11G20130.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
-----------------------------gtatgtttgattttcatta-ttgtgtccttcactatttcttttcttatggatatcaatttattttctcattagatagcaataaaaa-----cttgaatactcat--gcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
|| | |||| | | |||| | || | | | || |||| | | || | |||||| | || | || ||| | | | || |||||||| | ||||||||||||||||| || |||||||||||| || ||||||||||||||||||||||| ||||| |||||||||||||||||||||| |
gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgt-agccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
upper sequence: GLYMA11G20130.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G017334_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------gtatgtttgattttcattattgtgt--ccttcactatt----------tcttttcttatggatatcaatttattttctcattagatagcaataaaaacttgaatactcatgc-agATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
| | || | ||||| | | | ||| | | || || | | || ||| | | | || || | || | || | ||||||| || |||| |||||||||||| || ||||| || ||||| |||| | ||||||| ||| ||| || || |||||||||||||||||||| |
gtatgtgcttccagaaaactattcatttgcatttctttcctatcattccagctattgattcttttaggtcgtatcagacccactatattgcatttcttctgctaatagaagtggagttgttagttgta-acattcattgttaacttgcccaaattattctacatttccttttaattattccagATGGGTCTAATGAGGAAACATCCTTCGATCATACCTTTCATGATCTACATCTCTAATGAGGGTAAGCACACAGAGAGGTTTGCTGTACGTGCAAAGTACA
upper sequence: GLYMA11G20130.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0061g00280.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtttgattttcattattgtgtccttcactatttcttttcttatggatatcaatttattttctcattagatagcaataaaaacttgaatactcatgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
| || || | ||| | || | | | | || | | |||| | | | || ||| | || | | | |||||||||||| |||||||||||||| ||||| |||||||| |||||| |||| |||||||| || |||||||||||| |||||||||| |||||||||||||
--gtaagtgtcttcactaattctaattttttttttccttctcctgacaaggaatcttttagtgttttgtttt-tagttacaatggttgttccaattg-gcagATGGGGCTTATGAAGAAACATCCGTCAATCATACCATTCATGATATACATCACAAATGAAGACAAACACTTGGAACGATTTGCTGTTCGTGCAAAGTATA
upper sequence: GLYMA11G20130.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S7_501V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------gtatgtttgattttcattattgtgtccttcactatttcttttcttatggata--tcaatttattttctcat---tagatagcaataaaaacttgaatactca-----tgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
| | || ||| | | | | | || || | | | | | | || |||| || | | |||| | ||| | | | || |||||||| || |||||||||||||| || ||||| ||||| ||| | ||||| | || || || |||||| || ||||||||||||| |||||||| | |
gtaagtatataatttgaagctcggatacggttccttcattgcaaatctgattcagattaccgatttatgccctttagttccttcgatttcttgcgtagtctgtagagggtaatccgtattcttactcttggtttttgcagATGAAACTGATGAAGAAACATCCCTCGATTATTCCATTCATGGTGTACATTGCCAAGGAAGAAAAACACATGCAAAGATTTGCTGTTCGTGCAAAACAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatatcaatttattttctcattagatagcaataaaaacttgaatactcatgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
aatttattttctcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttgattttcattattgtgtccttcactatttcttttcttatggatatcaatttattttctcattagatagcaataaaaacttgaatactcatgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG