Sequence
atgc intronic sequence ATGC exonic sequence...gtgaaaccatggctttctttctatgcattgactttttaaggtttaattgctgtttggtgtgcaattttctaatactgctatattatttggatggatgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG
Basic information
species | Glycine max |
transcript | GLYMA20G35760.1 |
intron # | 2 |
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 2
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 4
----------------------------------gtgaaacc-atggctttctt--tct-atgcattgactttttaaggtttaattgctgtttggtgtgcaattttctaatactgctatattatttggatggatgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG
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gtatgtggaacgttagatgttttctctctgttgagtactactgatgaaattattagtctgatgtgttaaattgccaatatttt-ctgctaatgtatgaattagtacttaatctaactttcttgtcactctttg-gcagTCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAACATCTGTCATTGTTTTAG
upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g14929.1 (Oryza sativa), 3'ss of exon 4
-gtgaaaccatggctttctttctatgcattgactttttaaggtttaattgctgtttggtgtgcaattttctaatactgctatattatttgg-atggatgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG
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aatgaaactgca-cgtagctcctaaaccttgagctcttttcttagccctatt-ctcgatgctcagtcctgtattcctaatactttatgagttgtccatgcagTCTATGATTGAGCTAAGCCGCACACAGGATGAAGAAGTAGGAGATGGCACGACATCTGTTATTGTTCTTG
upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 4
----gtgaaaccatggctttctttctatgcattgactttttaaggtttaattgctgtttggtgtgcaattttctaatactgctatattatttggatggatgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG
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acccgtatatataccctaccatatttgtgtgctaa-tgtgcagtctatggttcatgttgtgagtcccatgtactta-attgtggttgtgtttaaatg--tgcagTCTATGATTGAACTAAGTCGTACACAAGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG
upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G069765_T02 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------------------gtgaaaccatggctttct-ttctatgcattgactttttaaggtttaattgctgtttggtgt-gcaattttctaatactgctatattatttggatgg-atgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG
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gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtgcagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG
upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G069765_T04 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------------------gtgaaaccatggctttct-ttctatgcattgactttttaaggtttaattgctgtttggtgt-gcaattttctaatactgctatattatttggatgg-atgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG------------------------------
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gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtgcagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT
upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
----gtgaaaccatggctttctttctatgcattgactttttaaggtttaattgctgtttggtgtgcaattttc-taatactgctatattatttggatggatgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG
| | | | || ||||| | | | ||| | |||| || || | || || || | | | | ||| || | || ||||| ||||||||||| || ||||| ||||||||||||||||| |||||||| || || ||||| ||||||
atttttttagcttttaaattttttctgt---tgggcttctgtcaatttagttcctcaaaactctgtcatcttagttgtgagttttttatatatgacttga--cagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgctgtttggtgtgcaattttctaatactgctatattatttggatggatgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG
ttctaat putative branch site (score: 2)
aattttctaatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaaccatggctttctttctatgcattgactttttaaggtttaattgctgtttggtgtgcaattttctaatactgctatattatttggatggatgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - -catggct
- - - - - - - - - - ctatgca
- - - - - - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgct