Sequence
atgc intronic sequence ATGC exonic sequence...cagacagttaaagatagatatcattaaataaaatgcttatgacgtcaacaaaggaggaaaattgatgtttattcaagtcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
Basic information
species | Glycine max |
transcript | GLYMA17G17010.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 2
-------------cagacagttaaagatagatatcattaaataaaatgcttatgacgtcaacaaaggaggaaaattgatgtttattcaagtcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
|| | | || | | | |||||| | | || || | | |||| | | | | | | | ||||| || ||||| ||||| || ||||| || ||||| ||||| || || || |||||||||||||| || ||||| ||||| ||||| ||
gtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaa--agttcttttactttggttgggggtgattagGTGGGTATGACATGGAGGAGAAAGCGGCGAGAGCGTATGACCTGGCGGCGCTCAAGTATTGGGGCCCTTCCACACACATCAACTTCCCG
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------cagacagttaaagatagata--tcattaaataaaatgcttatgacgtcaacaaaggaggaaaattgatgtttattcaagtcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
| | | ||| || | ||| | || || || | ||| | | | |||||| || ||| ||| ||||| |||||||||||||| || |||||||| |||| |||||||| |||||||||||||| ||||| ||||| ||||||| || || ||
gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgact--tctttatttttgtttgattaaatcttta---ttagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
cagacagttaaagatag-atatcattaaataaaatgcttatgacgtcaacaaaggaggaaaattgatgtttattcaagtcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
||||| | | | | | | ||| | | || | || | | | | || ||| ||| |||| | ||||||||||||||||||| |||||||||||||||||||||||||||||||| || ||||| |||||||||||||| || || || || || || ||
-tttcagtttatcttggtaagccttcttatagagaggttcaacatttaatcatacaccccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
cagacagttaaagatagatatcattaaataaaatgcttatgacgtcaacaaaggaggaaaattgatgttt---attcaag---tcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
| | | | | | | | | ||| || || || | || ||| ||| || || | || | |||||||||||| | ||||| ||||| || |||| |||||||| || || ||||||||||||||||| | || ||| |||||||||
-----aatgcgcagtttacctgggtgagtgtcactctt-tgttgttcgtgcttgaagttttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 3
cagacagttaaagatagatatcattaaataaaatgcttatgacgtcaacaaaggaggaaaattgatgttt---attcaag---tcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
| | | | | | | | | ||| || || || | || ||| ||| || || | || | |||||||||||| | |||||| ||||| || |||| |||||||| || || ||||||||||||||||| | || ||| |||||||||
-----aatgcgcagtttacctgggtgagtgtcactctt-tgttgttcgtgcttgaagtgttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAGGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacaaaggaggaaaattgatgtttattcaagtcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
ttttgat putative branch site (score: 4)
ctttt CT-rich tract
aaaattgatgtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagacagttaaagatagatatcattaaataaaatgcttatgacgtcaacaaaggaggaaaattgatgtttattcaagtcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - ggaggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaact