Sequence
atgc intronic sequence ATGC exonic sequencegtattatctactttgtgattttttttttctttttaaatattttaaagtttcgtcattgattttatttcacaattaacatgggtacatggaatgtagGATGATTTTGATGATGGATACGAGATGTATCATGTTCAAGGTACACTTAGAGAGTGGGTTACAAGAGATGAAGTGCGCCGCTTCATAGCCAGGAAATTCA
Basic information
species | Glycine max |
transcript | GLYMA17G03920.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 4
gtattatctactttgtgattttttttttctttttaaatattttaaagtttcgtcattgattttatttcacaattaacatgggtacatggaatgtagGATGATTTTGATGATGGATACGAGATG------TATCATGTTCAAGGTACACTTAGAGAGTGGGTTACAAGAGATGAAGTGCGCCGCTTCATAGCCAGGAAATTCA
||| | || | | || ||| || | || | ||| |||| | | | | || | || | ||| ||||||| |||||||| | | | |||||| || | ||| ||||| || |||||||||||||| |||||||||||||| |||||||| || || | ||
---gtattgatgtttgaactaaaattacctt---aagttcctttagattttccaattggtcgccgtcc-tatttgctgagcatattttatatgcagGATGAATTTGATGAAGAAGATGAGATGAACATGTACCGTGTACAAGGAACTCTTAGAGAGTGGGTCACAAGAGATGAAGTCCGCCGCTTTATCGCAAAGA------
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 4
------------------------------------gtattatctactttgtgattttttttttctttttaaatattttaaagtttcgtcattgattttatttcacaattaacatgggtacatggaatg-tagGATGATTTTGATGATGGATACGAGATG------TATCATGTTCAAGGTACACTTAGAGAGTGGGTTACAAGAGATGAAGTGCGCCGCTTCATAGCCAGGAAATTCA
| || | ||| | | || | ||| | | | | | | | || | || || | || ||||||| |||||||| | | | |||||| || | ||| ||||||||| | ||||||||||| |||||||||||||| || ||||| || || | ||
gtattgtcatatttatttaaactaggttattcagaacttgaattggttctgtaactaccaattaactagtaagccccatgttctgcagctctaaacgactgtctatcctttaattgactatcttttttggcagGATGAATTTGATGAAGAAGATGAGATGAACATGTACCGTGTCCAAGGTACATTGAGAGAGTGGGTCACAAGAGATGAAGTCCGTCGCTTTATTGCAAAGA------
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 3
gtattatctactttgtgattttttttttctttttaaatattttaaagtttcgtcattg--attttatttcacaattaacatgggtac---------atgga------atgtagGATGATTTTGATGATGG------ATACGAGATGTATCATGTTCAAGGTACACTTAGAGAGTGGGTTACAAGAGATGAAGTGCGCCGCTTCATAGCCAGGAAATTCA
|||| | | || || | | | | || ||| || || | || | | ||| ||| | | ||| | | | | |||| ||| |||||||| |||||||| | ||||||||| | ||||||||| || || || || |||||||| ||||||||||||||||||||||| || | ||
gtatcttgttctctgcagctctgatctcctatttccttaattcatagatgccccatcagaattgtgaattacatctcgtgtccattccttttactgatgggttcctcatgcagGATGATGATGATGATGATGGTGAGTTCGAGATGTACCGTGTTCAAGGAACGCTAAGGGAATGGGTTACTAGAGATGAAGTGCGCCGCTTCATTGCAAAGA------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaagtttcgtcattgattttatttcacaattaacatgggtacatggaatgtagGATGATTTTGATGATGGATACGAGATGTATCATGTTCAAGGTACACTTAGAGAGTGGGTTACAAGAGATGAAGTGCGCCGCTTCATAGCCAGGAAATTCA
aattaac putative branch site (score: 2)
attgattttatttcac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattatctactttgtgattttttttttctttttaaatattttaaagtttcgtcattgattttatttcacaattaacatgggtacatggaatgtagGATGATTTTGATGATGGATACGAGATGTATCATGTTCAAGGTACACTTAGAGAGTGGGTTACAAGAGATGAAGTGCGCCGCTTCATAGCCAGGAAATTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG