Sequence
atgc intronic sequence ATGC exonic sequencegttagaactgtttgtcttattttgttttgcctgaagttcacatgtccattgaaaagtaatgggaagtttgttcctggatattacatttcagGCTGTGTACCATATGCCAACAACTGAGAATGATATGCCCACTGGTAGCATCCCTTTGGCCTTACAAAGTTTATTCTACAAGCTTCAATACAGTGACACTA
Basic information
species | Glycine max |
transcript | GLYMA20G11300.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 1
gt-tagaactgtttgtcttattttgttttgcctgaagttcacatgtccattgaaaagtaatgggaagtttgttcctggatattacatttcagGCTGTGTACCATATGCCAACAACTGAGAATGATATGCCCACTGGTAGCATCCCTTTGGCCTTACAAAGTTTATTCTACAAGCTTCAATACAGTGACACTA
|| | | | || || || | | | |||| || |||| | | | | || |||| ||||||||||| ||||||||||| || || ||||||||||| |||| || || || ||||| || || || | ||||||||||| || || ||||||| ||
gtgtgagatcatgcatcataattcagagcattctagactattgtttcca----gaactaattga---ctaacttcattattttac---ccagGCTGTGTATCATATGCCAACCACCGAAAATGATATGCCATCTGGGAGTATTCCGTTGGCATTGCAGAGCCTTTTCTACAAGCTCCAGTATAGTGACAATA
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 5
gttagaactgtttgtcttattttgttttgcctgaagttcacatgtccattgaaaagtaatgggaagtttgttcctggatattacatttcagGCTGTGTACCATATGCCAACAACTGAGAATGATATGCCCACTGGTAGCATCCCTTTGGCCTTACAAAGTTTATTCTACAAGCTTCAATACAGTGACACTA
|| | || | ||||| || | | ||| | | ||| || | | | | || || | |||| ||||||| |||||||||||||| || |||||||||| || || |||||||||||||| || |||||| | |||| ||| ||||| | ||||||| ||
---------gtgaggctaaatttgtaaattct----cttaaatgaatccta-----tgatgcgaggctgatacagaga-atgatattttagGCTGTATACCATATGCCAACTACAGAGAATGATACACCTTGCGGGAGCATCCCTTTGGCTTTGCAAAGTCTTTTCTGCAAACTTCAGCATAGTGACAATA
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 5
gttagaactgtttgtcttattttgttttgcctgaagttcacatgtccattgaaaagtaatgggaagtttgttcctggatattacatttcagGCTGTGTACCATATGCCAACAACTGAGAATGATATGCCCACTGGTAGCATCCCTTTGGCCTTACAAAGTTTATTCTACAAGCTTCAATACAGTGACACTA
| || | | | || |||| | | || ||| | | |||| | || ||| || || || | ||||||| || ||||||||||||||||||||||| ||||| |||| || |||||||| ||| | || || | || |||||||| || || ||||||| |
-gtgaaatcaatcat--tgttctgttctacatgt--ttctctaagcacctgaa---ttttgaaccatttatt----gaaatgttttcatagGCTGTATATCATATGCCAACAACTGAGAATGACATGCCATCTGGGAGTATCCCTTTAGCCCTGCAGAGCCTGTTTTACAAGCTACAGTATAGTGACAACA
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 5
gttag-aactgtttgtcttattt-tgttttgcctgaagttcacatgtccattgaaaagt----aatgggaagtttgttcctggat-attacatttcagGCTGTGTACCATATGCCAACAACTGAGAATGATATGCCCACTGGTAGCATCCCTTTGGCCTTACAAAGTTTATTCTACAAGCTTCAATACAGTGACACTA
|||| ||| || |||| ||| | ||| || | || | | | | | | | || ||| | || ||||| || |||||||||||||||||||||||||| ||||||||||||||||| |||| ||||| |||||||| || || ||||||||||| ||||||||||||||||||| |
gttaataaccattgttcttttttctacattgtctctgttacatgtcttcttgaagatatttgaaaagggtaacaattttttggatcatgttttttcagGCTGTGTACCATATGCCAACGACTGAGAATGATATGCCATCTGGAAGCATTCCTTTGGCTTTGCAGAGTTTATTCTATAAGCTTCAATACAGTGACAGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcacatgtccattgaaaagtaatgggaagtttgttcctggatattacatttcagGCTGTGTACCATATGCCAACAACTGAGAATGATATGCCCACTGGTAGCATCCCTTTGGCCTTACAAAGTTTATTCTACAAGCTTCAATACAGTGACACTA
atattacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaactgtttgtcttattttgttttgcctgaagttcacatgtccattgaaaagtaatgggaagtttgttcctggatattacatttcagGCTGTGTACCATATGCCAACAACTGAGAATGATATGCCCACTGGTAGCATCCCTTTGGCCTTACAAAGTTTATTCTACAAGCTTCAATACAGTGACACTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT