Sequence
atgc intronic sequence ATGC exonic sequence...acctaatacaagatttacattctctgtcttgtttctatgattactttgataagcatagatgattggatgaatactaagatgtttgttataatgattttagATCTGGGATGCTTACAATGTGAAAGCACAAACATTTAAGACTGCCATTGAAGCTGCTTGCATGCTTCTGCGGATTGATGATGTAGTGAGTGGGATCAAGA
Basic information
species | Glycine max |
transcript | GLYMA20G35760.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 13
acctaatacaagatttacattctctgtcttgtttctatgattactttgataagcatagatgattggatgaatactaagatgtttgttataatgattttagATCTGGGATGCTTACAATGTGAAAGCACAAACATTTAAGACTGCCATTGAAGCTGCTTGCATGCTTCTGCGGATTGATGATGTAGTGAGTGGGATCAAGA
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--gttggcctttttctccatgtgcactgctgcatatatcctgcttttgttgtgtacacatta------aaacaccatagtattgcctt-----gtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA
upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 13
acctaatacaagatttacattctctgtcttgtttctatgattactttgataagcatagatgattggatgaata-ctaagatgtttgttataatgattttagATCTGGGATGCTTACAATGTGAAAGCACAAACATTTAAGACTGCCATTGAAGCTGCTTGCATGCTTCTGCGGATTGATGATGTAGTGAGTGGGATCAAGA
| | | || | | | | | | | | || ||| ||| || || |||| |||| | |||||||||||||||| | |||| ||| ||||||||||| || ||||| || ||||| ||||||||||||||| || | || ||||| | || || || |||||||
------------------gtatttctttttatgtgcacaaaagcatgcctgacca---atgtttgtttgcatgtctaaccacaatgttgt--ccattttagATCTGGGATTCCTACAGTGTTAAAGCACAAACGTTCAAGACAGCAATTGAGGCTGCTTGCATGCTTTTGAGAATCGATGACATTGTCAGCGGTATCAAGA
upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 13
acctaatacaagatttacattctctgtcttgtttctatgattactttgataagcatagatgattggatgaatactaagatgtttgttataatgattttagATCTGGGATGCTTACAATGTGAAAGCACAAACATTTAAGACTGCCATTGAAGCTGCTTGCATGCTTCTGCGGATTGATGATGTAGTGAGTGGGATCAAGA
|||| || | | | | | | | | | ||| || ||| || || | ||| || |||||||||||||||| | |||| || ||||| || || || ||||| || ||||| ||||||||||||||| || | || ||||| | || || || |||||||
----------------gtattccct---tcatctgcacaaatgcaagtttgaccat---tgtttgtttgcatgtctaaatgcc-acaatgcccattttagATCTGGGATTCCTACAGCGTTAAAGCGCAGACGTTCAAGACAGCGATTGAGGCTGCTTGCATGCTTTTGAGAATAGATGACATTGTCAGCGGTATCAAGA
upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 12
----------acctaatacaagatttacattctctgtcttgtttctatgattactttgataagcatagatgattgga---tgaatactaagatgtttgttata-atgattttagATCTGGGATGCTTACAATGTGAAAGCACAAACATTTAAGACTGCCATTGAAGCTGCTTGCATGCTTCTGCGGATTGATGATGTAGTGAGTGGGATCAAGA
|| | | | | | |||| || ||| || || | | | || ||| | || || | || | ||| | || | || || |||| ||||||||||| |||||||| ||||| || |||||||| ||||| || |||||||||||||| || |||| || || | |||||||| || || |
gttcgagattttcttctcctataatcctattcactttctaattgct-tcacaatttggatttttgtttttgtttttaatttgtgaaactggatactgcatacatatttttccagATATGGGATGCTTATAATGTGAAGGCACAGACCTTTAAGACCGCCATCGAGGCTGCTTGCATGCTGCTTAGGATCGACGACATCGTGAGTGGAATAAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgataagcatagatgattggatgaatactaagatgtttgttataatgattttagATCTGGGATGCTTACAATGTGAAAGCACAAACATTTAAGACTGCCATTGAAGCTGCTTGCATGCTTCTGCGGATTGATGATGTAGTGAGTGGGATCAAGA
ctttgat putative branch site (score: 5)
atgtttgttataatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acctaatacaagatttacattctctgtcttgtttctatgattactttgataagcatagatgattggatgaatactaagatgtttgttataatgattttagATCTGGGATGCTTACAATGTGAAAGCACAAACATTTAAGACTGCCATTGAAGCTGCTTGCATGCTTCTGCGGATTGATGATGTAGTGAGTGGGATCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - aatacaag
- - - - - - - - -cattctc
- - - - - - - - - - - - tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt