Sequence
atgc intronic sequence ATGC exonic sequencegttaggttctgctgctcatgaatcctgttgcttgattcaagatgactcaaatcagattttgctaattttgatgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
Basic information
species | Glycine max |
transcript | GLYMA12G02450.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g71320.1 (Oryza sativa), 3'ss of exon 6
------------gttaggttctgctgctcatgaatcctgttgcttgattcaagatgactcaaatcagattttgctaattttgatgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
|| | ||| | || | ||| ||| || || | |||| || || || | ||| |||| |||| ||||||||||||||||| |||||||||||||| || || | || || ||| || ||| | | || |||||| | |||| | | ||
gtagcaacctgggtaaaattcaattattctggtatcttgtgttgtggttta----gactgaa--cactttgtacta-ccatgattcagGGCTTTGAGAAAATGATATCAGGAATGTATCTTGGGGAAATTGCAAGATTGGTATTTCATAGAATGGCCCAGGAATCAGATGTTTTTGGTGATGCTGCTG
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g31110.1 (Oryza sativa), 3'ss of exon 6
gttagg--ttctgctgctcatgaatcctgttgcttgattcaagatgactcaaatcagattttgctaattttgatgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
|| || ||||| ||| || | ||| || | | |||| | | ||||| | |||||||||||||||||||||| ||||| |||||||||| || || | || || | | || ||| | |||||||||||| |||| || | |
gtaagaccttctgaaaaatgggaagtttggagtttgtgataattaggccgaaattaatgtcatttaatt--ggtgtagGGTTTTGAGAAAATGATCTCTGGTGTGTATCTTGGGGAAATTGCAAGATTGGTGTTCCAAAAAATGGCTGAAGAGTCAGATATATTTGGTACTGCTGTTG
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------gttaggttctgctgctcatgaatcctgttgcttgattcaagatgactcaaatcag-at--tttgctaattttgatgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
||| | | | | | || ||| | | || | | | | |||| || |||| || | | ||||| |||||||| |||||||| ||||||||||| |||||||| || | ||||| ||||| | ||||| ||| || ||||| ||||||| || ||
gtaatctttgccatacttccctgtttttccgatttggtattgcgttattagtttttaaccaattaacatcaacatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0061g00040.t01 (Vitis vinifera), 3'ss of exon 6
gttaggttctgctgctcatgaatcctgttgcttgattcaagatgactcaaatcagattttgctaattttgatgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
|| |||| | || | | | ||| || ||| || |||||||| ||||| | |||||||||||||||||||||| || ||||| | |||||||| ||||||||||| ||||| || ||||| | |||||||| || |||||||| ||||||
gtacagttcaattacttgcccttgtctcttcgatgttccag-tgaacaaatcaagattttgaggcttttgtttcagGGTTTTGAGAAAATGATATCAGGGATGTACTTGGGTGACATTGTGAGGAGAGTTATTCTCAGAATGTCACAGGAGTCAGACATTTTTGGACCTGTTTCTT
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S58_165V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------gttaggttctgctgctcatgaatcctgttgcttgattcaaga--tgactcaaatcagattttgctaattttgatgtagGGT--TTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
| | || | | | | || | || ||||| ||| || | | | ||||| | |||| || |||||||||||||||||||| ||||| ||||| || |||||| | || || |||||| | ||| | | || |||| | |
gtgcgaacttttaccaaacagttgaagtgagtgcacatgagagttgtttcactcggtgcccatcatac-atccaagagctgaatcc--ttgggtccctctaatctccatgtgcagTGGTTTGAGAAAATGATATCTGGGATGTACCTTGGCGAGATCGTGCGTCTCGTGCTTGCGAGGATGGCTGAAGAAGCGCAGTTGTTTGGTGGCAGCCCCC
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ14634 (Selaginella moellendorffii), 3'ss of exon 6
gttaggttctgctgctcatgaatcctgttgcttgattcaagatgact-caaatcagattttgctaattttgatgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
|| | || | || | | | | || ||| || ||||| |||||||| || | || ||||||||||| |||||||| |||||||| |||||||| | | | ||| || | | |||| |
--------------------------gtgagatacttgcaattgcttgtacagctgacgcagctgtgcctg--gtagGCGTTTGAGAAGCTGTTTTCGGGAATGTATCTGGGTGACATTGTGAGGAGGGTCATTCTCAAGCTTGCGCAGGATGCCTGCCTATTTGGCGGCAGCATAC
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ25912 (Selaginella moellendorffii), 3'ss of exon 6
gttaggttctgctgctcatgaatcctgttgcttgattcaaga-tgactcaaatcagattttgctaattttga--tgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
|| | || | ||| | | || | | | | | | ||| ||||| || ||||| ||||||||||||||||| || |||||||| ||||||||||| | | || | || | | | ||||| |
------------------gtaagcttgaaaatgaccacaaaaacaattcctaccctaccctacctgtgttggactgtagATATTCGAGAAGATGATATCTGGAATGTACCTGGGTGACATTGTGAGGAGAGTGTTGTGGAAACTGGCTGCCGAAGCGGCATTCTTTGGAGGAAAGGTAC
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ10895 (Selaginella moellendorffii), 3'ss of exon 6
gttaggttctgctgctcatgaatcctgttgcttgattcaaga-tgactcaaatcagattttgctaat-tttga-tgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
|| | || | ||| | | || | | | | | | ||||| ||||| || ||||||||||||||||||||||| || |||||||| ||||||||||| | | || | || | | | ||||| |
------------------gtaagcttgaaaatgaccacaaaaacaattcctaccctaccctacctgtgtttgactgtagATATTCGAGAAAATGATATCTGGAATGTACCTGGGTGACATTGTGAGGAGAGTGTTGTGGAAACTGGCTGCCGAAGCGGCATTCTTTGGAGGAAAGGTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcctgttgcttgattcaagatgactcaaatcagattttgctaattttgatgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
attttgctaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaggttctgctgctcatgaatcctgttgcttgattcaagatgactcaaatcagattttgctaattttgatgtagGGTTTTGAGAAAATGATATCTGGAATGTATCTTGGTGACATCGTGAGGAGAGTCATTCTAAGGATGTCGCTAGAGTCAGATATGCTTGGACCTATTTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG