Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcctttttggttcccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtattttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
Basic information
species | Glycine max |
transcript | GLYMA07G40230.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 6
---------------gtatgtcctttttggttcccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtattttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
| || ||| | | | | | | | | || ||| ||| | || || | || || | | | | | || | ||||||||| ||||||||||| ||||||||||| |||| |||||||||||| ||||| || |||| || || ||| ||| | || || |||||||||||
aggatgaggaagatgatgagtacttaattgatgctcttacagtaata--gataaatgttatctgtttacttgatcaaaatatgtt---ttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 8
gtatgtcctttttggttcccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtattttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
||| || || | | | |||| | | | || ||| ||| || || | || || | | | | | || | ||||||||| ||||||||||| ||||||||||| |||| |||||||||||| ||||| || |||| || || ||| | ||| | || || |||||||||||
gtacgtaatt---gatgctctta-cagtaata--gataaatagcatctgtttacttgatcaaaatatgtt---ttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATCTGCAATTATAGTATCTCGTCCTGAA
upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 8
gtatgtc-ctttttggttcccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtattttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
||| ||| || || | | | | | | || |||||||| || | | | | |||| | | || | ||| | |||||||||||||||||| || ||||||||||| |||| |||||||||||| || || ||| |||| || || || | ||| | || || |||||||||||
gtacgtcactattatgctgacagcgattccatacagattaattagctccagtttgtgtaattaaa-acttttaacattttgt----tccagTGAGAGTGCAAATGAGTACACAGATGATGAGGATGCAAGCTGGAAAGTCCGTAGGGCATCAGCAAAGTGCCTATCTGCAATTATAGTGTCTCGTCCTGAA
upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G053644_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------gtatgtcctttttggttcccttagctgca---gtatgg--attaattctttcatgatattcttgttaatcatctcaaatgtgctg-tattttg---cagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
| || ||| | | | || | || |||| | || || |||| | | || || | | ||| | | |||||| |||||||||||||||||| || ||||||||||| |||| |||||||||||| || || ||| || | || || || | ||| | || || |||||||||||
gtatgttcccctatttttgcgacttatggtgatgtcccttgctgtctcggcaataaagtatcaccagactgcaggatttaggccgcccaggtccaattgtattgtaataaaaacttttaaactggtcagtttgtgtaattaaaactttttaacattttgttccagTGAGAGTGCAAATGAGTACACAGATGATGAGGATGCAAGCTGGAAAGTCCGTAGGGCATCATCAAAGTGCCTATCTGCAATTATAGTGTCTCGTCCTGAA
upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgtcctttttggttcccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtatttt---gcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
|| || || || | | | | | | || || || | | | | ||| || |||| | | ||| ||| |||||||||||||| || |||||||||||||||| |||||||||||| |||||||||| || ||||| |||||| ||| || ||||| ||| |||||
----gtaagttctgatttattcattggaacagtagcctagctcctt-acggtgcacc-attatctcactgaaataagtctttctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 9
gtatgtccttt-ttggttc-------ccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtat------tttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
|||||| || ||||| | |||| || | || |||| | |||| | |||||| | || ||| | || |||||| |||| ||||||||||||| |||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||| |||||||| |||||||||||||| |||||
gtatgttgttcactggtttatgtatatttgagctatcgtgtaaat-aatttatgcatgcttgaattgttactaatatcaca-gtactgtatcttgtatttgtagTGAGAGTGCAACTGAATATACAGATGATGAGGATGTCAGCTGGAAAGTTCGAAGAGCAGCAGCTAAATGCTTAGCAGCTTTGATTGTTTCTCGACCTGAA
upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S337_6V6.1 (Physcomitrella patens), 3'ss of exon 7
--------gtatgtcctttttggttcccttagctgcagtatggattaattctttcatg-atattcttgttaatcatctcaa--atgtgctgtattttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
| | ||| | | || | ||| | | | | |||| || | | | | || || ||| | | ||||| ||||||||| |||| |||| |||||||||||| | ||||||||||| || || || |||||||| || ||| | || | || ||| | ||||||
ccttacttgcagaataagcttgagaactgcatctcttg-atgtttcactcttatcattcatgtcttcgacgggagatttaactatctgcgtttctgtgcagGGAGAGTGCAGATGAGTATAGTGATGATGAAGATATGAGCTGGAAAGTACGAAGGGCTGCAGCTAAGTGCTTATCGGCTGTAATCTCTTCGAGACCTGAG
upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ33911 (Selaginella moellendorffii), 3'ss of exon 7
gtatgtcctttttggttcccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtattttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
||| | || ||| | || || | || || | | ||| | | | ||| ||||| || | || || | || |||||||||||||||||||| || |||||||| ||||| ||||| | | ||| | || || | || |||
-----------------------------gtaggtttttattacgtttccccatcctgctgaagtatt----aagagctatgtct--cagGGAGAGCGCTGACGAGTACAGTGACGATGAAGATGTAAGCTGGAAGGTGCGGAGAGCTGCAGCAAAATGCCTTTCTGCAGTTATCTCATCGAGACCGGAG
upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ37421 (Selaginella moellendorffii), 3'ss of exon 7
gtatgtcctttttggttcccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtattttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
||| | || ||| | || || | || || | | ||| | | | ||| ||||| || | || || | || |||||||||||||||||||| || |||||||| ||||| ||||| | | ||| | || || | || |||
-----------------------------gtaggtttttattacgtttccccatcctgctaaagtatt----aagagctatgtct--cagGGAGAGCGCTGACGAGTACAGTGACGATGAAGATGTAAGCTGGAAGGTGCGGAGAGCTGCAGCAAAATGCCTTTCTGCAGTTATCTCATCGAGACCGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaattctttcatgatattcttgttaatcatctcaaatgtgctgtattttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
tgttaat putative branch site (score: 3)
atattcttgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcctttttggttcccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtattttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT