Sequence
atgc intronic sequence ATGC exonic sequencegtgaggttcggcatttgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATTGTGAGAAGAGTCATTCTTAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
Basic information
species | Glycine max |
transcript | GLYMA01G43650.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g71320.1 (Oryza sativa), 3'ss of exon 6
--gtgaggttcggca---tttgatgactcctgttgcttgatttgtcat---gactaaa-attttggag-atttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATTGTGAGAAGAGTCATTCTTAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
| | || | || || | || || |||| |||| | |||| || | |||| | | | | ||||| |||||||||||||||||||||||||||||||| || |||| ||| || ||| || ||| | || || ||| | ||||| | ||
gtagcaacctgggtaaaattcaattattctggtatcttgtgttgtggtttagactgaacactttgtactaccatgattcagGGCTTTGAGAAAATGATATCAGGAATGTATCTTGGGGAAATTGCAAGATTGGTATTTCATAGAATGGCCCAGGAATCAGATGTTTTTGGTGATGCTGCTG
upper sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------gtgaggttcggcatttgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATTGTGAGAAGAGTCATTCTTAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
| | || || ||| | | | | || | || ||| | | |||| || | || |||| |||||||| |||||||||||||||||||| ||||||||||| | ||||| ||||| |||||| ||| || ||||| |||||||| || || |
gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatcaacatcattt-ggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
upper sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0061g00040.t01 (Vitis vinifera), 3'ss of exon 6
gtgaggttcggc-atttga---tgactcct-gttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATTGTGAGAAGAGTCATTCTTAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
|| |||| | ||| || ||| | | || | | | || | || |||||| | ||| | | |||||||||||||||||||||||||| ||||| | |||||||||||||| ||||| ||||| | |||||| ||||| || || |||||||| |||||
gtacagttcaattacttgcccttgtctcttcgatgttccagtgaaca-aatcaagattttgaggcttttgtttcagGGTTTTGAGAAAATGATATCAGGGATGTACTTGGGTGACATTGTGAGGAGAGTTATTCTCAGAATGTCACAGGAGTCAGACATTTTTGGACCTGTTTCTT
upper sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ14634 (Selaginella moellendorffii), 3'ss of exon 6
gtgaggttcggcatttgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtg-cagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATTGTGAGAAGAGTCATTCTTAAGATGTCATTAGAGTCGGATATGTTTGG-ACCAATTTCTC
| ||| | | ||||||| | || | | || | || || ||| |||||||| || | || ||||||||||| |||||||||||||| || |||||||| ||| | | || | | ||||| || |
------------gtgagatacttgcaattgcttg------tacagctga-----cgcagctgtgcctggtagGCGTTTGAGAAGCTGTTTTCGGGAATGTATCTGGGTGACATTGTGAGGAGGGTCATTCTCAAGCTTGCGCAGGATGCCTGCCTATTTGGCGGCAGCATAC-
upper sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ25912 (Selaginella moellendorffii), 3'ss of exon 6
gtgaggttcggcatttgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATTGTGAGAAGAGTCATTCTTAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
|| || || ||||| | | | | | | | | | || | || || || ||||| |||||||| |||||||| || |||||||||||||| ||||| | || || | || ||| | |||||| || |
gtaagcttgaa-----aatgaccacaaaaacaattcctaccctaccctacctgt-----gttggactgtagATATTCGAGAAGATGATATCTGGAATGTACCTGGGTGACATTGTGAGGAGAGTGTTGTGGAAACTGGCTGCCGAAGCGGCATTCTTTGGAGGAAAGGTAC
upper sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ10895 (Selaginella moellendorffii), 3'ss of exon 6
gtgaggttcggcatttgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATTGTGAGAAGAGTCATTCTTAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
|| || || ||||| | | | | | | | | | |||| || || || |||||||||||||| |||||||| || |||||||||||||| ||||| | || || | || ||| | |||||| || |
gtaagcttgaa-----aatgaccacaaaaacaattcctaccctaccctacctgt-----gtttgactgtagATATTCGAGAAAATGATATCTGGAATGTACCTGGGTGACATTGTGAGGAGAGTGTTGTGGAAACTGGCTGCCGAAGCGGCATTCTTTGGAGGAAAGGTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATTGTGAGAAGAGTCATTCTTAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
gactaaa putative branch site (score: 2)
atgactaaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggttcggcatttgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATTGTGAGAAGAGTCATTCTTAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG