Sequence
atgc intronic sequence ATGC exonic sequence...gccttgccataatttaggagctttttggttcagtgagtagcaaacttgctccttgccctgatttattattggttataactatcttgtttccttgtttcagGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTATG
Basic information
species | Glycine max |
transcript | GLYMA09G39870.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39870.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 4
----gccttgccataattta--ggagctttttggttcagtgagtagcaaacttgctccttgccctgatttattattggttataactatcttgtttccttgtttcagGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTATG
|| | | || | | | ||| || || | | | | || || |||| ||| | || | | | | | || ||| |||||||| |||||||| || |||| ||||| || |||||||| || | ||||| ||||||||||||||||| || |||||||| || |||||||| | ||||
ataaatatttctacaaaccattgaaacttcatgcagca-taattggttccatttctgcttgtgttga---acctctgcatctgattggccg--ttgcttatttcagGTTGACATGATAGTTGTGACTGATGGGAGCCGTATTCTAGGTCTAGGTGATCTTGGAGTTCAGGGCATAGGTATACCTATCGGTAAACTTGATGTTTATG
upper sequence: GLYMA09G39870.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 4
-----gccttgccataattta-ggagctttttggttcagtgagtagcaaacttgctccttgccctgatttattattggttataactatcttgtttccttgtttcagGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTATG
| | | ||| | | || || | | ||| | | |||| | | || | ||| | ||| | || | | ||| |||||||| |||||||| || |||| ||||| ||||| ||||| ||||| ||||||||||| ||||||||||| || |||||||| || ||||| || | ||||
ctttagtcataccaaaccaaacggggcctaatatgtcaatatgcagcatgcattcttccaattctggctg--tatca--tgcaagtggttgaca--cttttttcagGTTGACATGATAGTTGTGACTGATGGGAGTCGCATTCTAGGCTTAGGTGACCTTGGTGTTCAGGGCATAGGTATACCTATTGGTAAACTGGATGTTTATG
upper sequence: GLYMA09G39870.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 4
-----gccttgccataatttaggagctttttggttcagtgagtagcaaacttgctccttgccctgatttattattggttataactatcttgtttccttgtttcagGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTATG
| | || || | | |||||| || ||| || ||| || || | | || ||| | || | | || |||| ||||| |||||||| || | |||||||| |||||||||||||| |||||||||||||||||||||| |||||||| ||||| || |||||||| |||||||
agtaaaaatggttgta--ttcagcattctttggtggcaggattag--gtttttctcactgttcttgtcttataatggacgtt-ctgtttctcttatgtgttgcagGTGGACATGATAGTGATAACAGATGGCAGTCGTATTCTTGGTCTGGGTGACCTTGGAGTTCAGGGAATTGGAATTCCTATTGGGAAACTTGATATGTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgctccttgccctgatttattattggttataactatcttgtttccttgtttcagGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTATG
ttataac putative branch site (score: 2)
tcttgtttccttgttt putative PPT
atttattattggttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccttgccataatttaggagctttttggttcagtgagtagcaaacttgctccttgccctgatttattattggttataactatcttgtttccttgtttcagGTAGACATGATTGTCTTGACAGATGGTAGTCGTATTCTTGGCTTGGGTGACCTTGGAGTTCAGGGCATTGGAATACCTATAGGAAAACTTGACATGTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
-ccttgcc
- - - - - - - - - - - - - - ttcagtg