Sequence
atgc intronic sequence ATGC exonic sequencegtaagctcatagttgtatttttgccatcctgttatattttttttttgtacttcattaacatctttcttctactagTGAATTTGGAGCTAAGGTAGTACCACCCAAAAAAATATTGAAGATGCTTCCTGAGCTGTTTGATCATCCAGATCAGAATGTTCGGGCTTCATCCAAGGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60040.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 4
gtaagctcatagttgtatttttgccatcctgttatattttttttttgta---cttcattaacatctttcttctactagTGAATTTGGAGCTAAGGTAGTACCACCCAAAAAAATATTGAAGATGCTTCCTGAGCTGTTTGATCATCCAGATCAGAATGTTCGGGCTTCATCCAAGGGT
||| | || ||| | | ||| | |||| | | || ||||| | | ||||| |||| ||| |||| ||||||||| |||||||||| ||||||||||| || |||||||||| |||||||||||||| |||||||| |||||||| |||||||| || ||||||
gtatgttcctagctagttcttttactccctgatttcgcaagttcttgtaaactcttaccaacatgtttcctctgctagCGAATTTGGAACTAAGGTAGTGCCACCCAAAAAGATTCTGAAGATGCTACCTGAGCTGTTTGACCATCCAGACCAGAATGTCCGGGCTTCTTCTAAGGGT
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G070126_T01 (Zea mays), 3'ss of exon 4
gtaagctcatagttg---tatttttgccatcctgttatattttttttttgt--act-tcattaacatctttcttctactagTGAATTTGGAGCTAAGGTAGTACCACCCAAAAAAATATTGAAGATGCTTCCTGAGCTGTTTGATCATCCAGATCAGAATGTTCGGGCTTCATCCAAGGGT
||| | || | | || | |||| | ||| | | | || |||| ||| | | |||||||||| ||| |||| ||||||||| |||||||||| ||||||||||| || ||||||||||||| ||||||||||| |||||||| |||||||| |||||||| || ||||||
gtatgttcctggctggttcttctttggctcactgatttggtaagttcttgtcaactcttaccaacatctttcctctgctagCGAATTTGGAACTAAGGTAGTGCCACCCAAAAAGATTCTGAAGATGCTTCCGGAGCTGTTTGACCATCCAGACCAGAATGTCCGGGCTTCTTCTAAGGGT
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 4
----gtaagctcatagttg-------tatttttgccatcctgttatattttttttttgtacttcat-----taacatctttctt-ctactagTGAATTTGGAGCTAAGGTAGTACCACCCAAAAAAATATTGAAGATGCTTCCTGAGCTGTTTGATCATCCAGATCAGAATGTTCGGGCTTCATCCAAGGGT
| || ||| | | || ||| | || || | |||||||| || | | || || || ||| | || ||||||| ||||| || || | || || || |||| ||| |||||||||||||| || || |||||||||| |||||| |||||||| || || || || ||
gtttggaatctctttgatgcaacatatataatacttgtctcttttttttttttttatgaatcttatacaattattattttttatgctgctagTGATTTTGGTGCAAAAATTGTGCCCCCAAAAAGAATTTTGAAGATGCTTCCAGAACTCTTTGATCATCAAGATCAAAATGTTCGTGCATCCTCTAAAGGG
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G29520.1 (Glycine max), 3'ss of exon 1
----gtaagctcatagttgtatttt-tgccatcctgttatattttttttttgtact---tcattaacatctttctt-ctactagTGAATTTGGAGCTAAGGTAGTACCACCCAAAAAAATATTGAAGATGCTTCCTGAGCTGTTTGATCATCCAGATCAGAATGTTCGGGCTTCATCCAAGGGT
| | ||| | | || | | | || || || | ||||| | | | |||| || ||| | || ||||||| |||||||| || | || || || |||| ||| |||||||||||||| || || |||||||||| |||||| |||||||| || || || || ||
gtttgagatctctttgatgcaacatatataatacttttctttttttaatgaatgttaaacaattattattttttatgctgctagTGATTTTGGAGCAAAAATTGTGCCCCCAAAAAGAATTTTGAAGATGCTTCCAGAACTCTTTGATCATCAAGATCAAAATGTTCGTGCATCCTCTAAAGGG
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 4
----gtaagctcatagttgta---tttttgccatcctgttatattttttttttgtacttcat-----taacatctttctt-ctactagTGAATTTGGAGCTAAGGTAGTACCACCCAAAAAAATATTGAAGATGCTTCCTGAGCTGTTTGATCATCCAGATCAGAATGTTCGGGCTTCATCCAAGGGT
| || ||| | |||| | | | | | | | | ||||||||| | | || || || ||| | || ||||||| |||||||| || | || || || |||| ||| |||||||||||||| || || |||||||||| |||||| |||||||| || || || || ||
gtttggaatctctttgttgcaacatatataatacttgtctttttcttttttttgaatcttatacaattattattttttgtgctgctagTGATTTTGGAGCAAAAATTGTGCCTCCAAAAAGAATTTTGAAGATGCTTCCGGAACTCTTTGATCATCAAGATCAAAATGTTCGTGCATCCTCTAAAGGG
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0116g00490.t01 (Vitis vinifera), 3'ss of exon 4
---------gtaagctcatagttgtatttttgccatcctgttatattttt----tttttgtacttcattaacatctttcttctactagTGAATTTGGAGCTAAGGTAGTACCACCCAAAAAAATATTGAAGATGCTTCCTGAGCTGTTTGATCATCCAGATCAGAATGTTCGGGCTTCATCCAAGGGT
| | || | | || | | | | | |||| || |||| |||||||| | ||| | | ||||||||||| || ||||| || ||||| |||| ||| ||||| ||||||||||| || || ||||||| ||| || |||||||| || || || || ||
gtttgtgcattgatttctttgctggaaactctgctttattttatgcttagctgattttcagacttcattgttgtgtttgta--atcagTGAATTTGGGGCGAAGGTTGTTCCACCAAAAAGAATTTTGAAAATGCTTCCTGAACTCTTCGATCATCAAGACCAAAATGTTCGTGCATCCTCTAAAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgccatcctgttatattttttttttgtacttcattaacatctttcttctactagTGAATTTGGAGCTAAGGTAGTACCACCCAAAAAAATATTGAAGATGCTTCCTGAGCTGTTTGATCATCCAGATCAGAATGTTCGGGCTTCATCCAAGGGT
cattaac putative branch site (score: 2)
catctttcttctact CT-rich tract
ttatattttttttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctcatagttgtatttttgccatcctgttatattttttttttgtacttcattaacatctttcttctactagTGAATTTGGAGCTAAGGTAGTACCACCCAAAAAAATATTGAAGATGCTTCCTGAGCTGTTTGATCATCCAGATCAGAATGTTCGGGCTTCATCCAAGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA