Sequence
atgc intronic sequence ATGC exonic sequence...aaaaaaaaatgtagccaagcatcttgcatggctgactttggaattttactttcttgttcctcttttttaaattctgactagcttaatttatggtttttagGCATATTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAATTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAA
Basic information
species | Glycine max |
transcript | GLYMA14G00940.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G00940.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 4
-aaaaaaaaatgtagccaagcatcttgcatggctgactttggaatttt-actttcttgttcctcttttttaaattctgactagcttaatttatggtttttagGCATATTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAATTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAA
|| || || | ||| ||| ||| | ||| || | ||| ||| | | ||| | || | | ||| | | | ||| | |||| || || || |||||||||||||| ||||||||||| || || ||||||||||| || |||||||||||| ||| || |||||
caactaaggattctgttttacataaaccataaaatactgtagaaattagaaattcctgtcggaatggtgcttatt-tatcttggtaaatgt-tcactcacagGTACGTTTTAGAGTCTGACCACATGAAGAAGTTCTTTGACTATATACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG
upper sequence: GLYMA14G00940.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 4
aaaaaaaaatgtagccaagcatct-tgcatggctgactttggaattttactttcttgttcctcttttttaaattctgactagcttaatttatggtttttagGCATATTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAATTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAA
| | | || | | ||| |||| | ||||| || | || ||| ||| | | | || | || | || ||| || |||| || || || |||||||||||||| ||||||||||| ||||| ||||||||||| ||||| || |||||| || || |||||
agctagacatcca-tgatccataagtgcaaaatttttgttggagttggaagctcctgtggacttttggtgctattttcttatagaacttgttcattgacagGTATGTTTTAGAGTCTGAACACATGAAGAAGTTCTTTGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG
upper sequence: GLYMA14G00940.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
aaaaaaaaatgtagccaagcatct-tgcatggctgactttggaattttactttcttgttcctcttttttaaattctgactagcttaatttatggtttttagGCATATTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAATTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAA
| | || | | || ||| |||| | | | || | | || ||| ||| | | | || | | | || ||| || |||| || || || || ||||||||||| || |||||||| ||||| ||||||||||| ||||| || |||||| ||| || |||||
-attactaagttggacatccataagtgcaaaaatattgtcgaaactagaggctcatgtggacttttggtgctattttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
upper sequence: GLYMA14G00940.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0057g00410.t01 (Vitis vinifera), 3'ss of exon 4
aaaaaaaaatgtagccaagcatcttgcatggctgactttg-gaattttactttcttgttcctcttttttaaattctgacta---gcttaatttatgg----tttttagGCATATTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAATTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAA
| || | | || || | || | |||| || | | | || ||||| || | | ||||||| ||| || ||| || | |||||||||| || ||||||||||||||||| ||| | || |||| ||||||||| ||||||||||| | |||||||||||
-------ctctgaattgtctattccacctctctctgttggtaaactatactcagttactaat-tagttcaaattgtgtccacatatttaatttctggatcacttgcagGTATGTGTTGGAATCAGCACAGATGAAGAAGTTTTTTGATTATGTACAAAACCCAACTTTTGAAATTGCATCAGATGCCGCAGCAACTTTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactttcttgttcctcttttttaaattctgactagcttaatttatggtttttagGCATATTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAATTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAA
ttttt CT-rich tract
ttaatttatggttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaaaaaatgtagccaagcatcttgcatggctgactttggaattttactttcttgttcctcttttttaaattctgactagcttaatttatggtttttagGCATATTTTGGAATCAGAGCACATGAAGAAGTTTTTTGACTATATTCAGCTACCAAATTTTGAAATAGCATCAGATGCTGTTGCAACTTTTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
aaaaaaa
- - - - - - - -caagcat
- - - - - - - - - - - - -gcatggc
- - - - - - - - - - - - - - - - -gactttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgac