Sequence
atgc intronic sequence ATGC exonic sequencegtatcgaattgagcagctcttttgttggcctttttcgccatcacttgttctatttctataatgacagaacaaatcatgcagATAAATTTGCGGTCTGCCCAAACAAATGCAGCATTTCGGAAACTCTTTAACCTCCCACCGGAAGAGTTTCTCATCGATGATTTTACCTGCCATCTAAAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g40570.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G372877_T01 (Zea mays), 3'ss of exon 4
---------------------gtatcgaattgagcagctcttttgttggcctttttcgccatcacttgttctatttctataatgacagaacaaatcatgcagATAAATTTGCGGTCTGCCCAAACAAATGCAGCATTTCGGAAACTCTTTAACCTCCCACCGGAAGAGTTTCTCATCGATGATTTTACCTGCCATCTAAAAC
| | |||| | | | || | | || || || | | | | | || || ||| | ||||||||||||||||||| ||||||||||| | ||||| ||||| || || |||||| | ||||||||| |||||||| ||||| ||||||||||| ||||
gtaagggatttaccacagttctttctgtgctgagaaagctgatcggcgggcgtactc-ccgtc-ttcagccgctcacagcagtg-taggacatgt-gtgcagATAAATTTGCGGTCAGCCCAAACAAACGTTGCATTCCGGAAGCTGTTCGCCCTCCCTCTGGAAGAGTTCCTCATCGACGATTTCACCTGCCATCTCAAAC
upper sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G00850.1 (Glycine max), 3'ss of exon 6
-------------------------------gtatcgaattgagcagctcttttgttggcctttt-tcgccatcacttgttctatttctataatgacagaacaaatcatgcagATAAATTTGCGGTCTGCCCAAACAAATGCAGCATTTCGGAAACTCTTTAACCTCCCACCGGAAGAGTTTCTCATCGATGATTTTACCTGCCATCTAAAAC
| | || | | || | | |||| || || | ||| | ||| | | | | || || |||| |||||||||||| | ||||||||| |||| |||| |||||||||| || ||||| || || ||||||||| |||| || ||||| ||| | |||
gtaaggatccatctatgttgtcaggcatttgtttttatgtttaattttttttctacttctgttttatcacccttttttgccttctttttctttttctatttacaaaattgtagATTAATTTGCGGTCTCCTCAAACAAATTCAGCCTTTCAGAAACTCTTTGGGCTTCCACCTGAGGAATTTCTCATCAATGACTTCACCTGTCATTTGAAAA
upper sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G39920.1 (Glycine max), 3'ss of exon 5
-------------------------------gtatcgaattgagcagctcttttgttggcctttt-tcgccatcacttgttctatttctataatgacagaacaaatcatgcagATAAATTTGCGGTCTGCCCAAACAAATGCAGCATTTCGGAAACTCTTTAACCTCCCACCGGAAGAGTTTCTCATCGATGATTTTACCTGCCATCTAAAAC
| | || | | || | | |||| || || | ||| | ||| | | | | || || |||| |||||||||||| | ||||||||| |||| |||| |||||||||| || ||||| || || ||||||||| |||| || ||||| ||| | |||
gtaaggatccatctatgttgtctggcatttgtttttatttttaattttttttgtacttctgttttatcacccttttctgtcttctttttgtttttctatttacaaaattgtagATTAATTTGCGGTCTCCTCAAACAAATTCAGCCTTTCAGAAACTCTTTGGGCTTCCACCTGAGGAATTTCTCATCAATGACTTCACCTGTCATTTGAAAA
upper sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 4
gtatcgaattgagcagctcttttgttggcctttttcgccatcacttgttctatttctataatgacagaacaaatcatgcagATAAATTTGCGGTCTGCCCAAACAAATGCAGCATTTCGGAAACTCTTTAACCTCCCACCGGAAGAGTTTCTCATCGATGATTTTACCTGCCATCTAAAAC
| | ||| | |||| |||| || | || || |||| || |||| |||||||||||| | ||||||||| ||||||||| |||||| ||| || ||||| || || ||||||||| ||||||| ||||| ||| | |||
--------------------------gtcacccttctttctgacttattcttttgtttta-------aaaaaat--tgtagATTAATTTGCGGTCTCCTCAAACAAATTCAGCATTTCAGAAACTGTTTGGGCTTCCACCTGAGGAATTTCTCATCAATGATTTCACCTGTCATTTGAAAA
upper sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------gtatcgaattgagca-gctcttttgttg-gcctttttcgccatcacttgttctatttctataatgacagaacaaatcatgcagATAAATTTGCGGTCTGCCCAAACAAATGCAGCATTTCGGAAACTCTTTAACCTCCCACCGGAAGAGTTTCTCATCGATGATTTTACCTGCCATCTAAAAC
| || || | | | | |||| | |||| | | | | | || | | ||| | ||| ||||||||||| ||| ||||| | ||||||||| | ||||||| |||||||||| || ||||| || || ||||||||| |||||||||| || || | ||||
gtaaatgactagcttttatggtcttaaattcactttgtgaggggactatgtttatgtgttctgactttcttgtc-tgatttacttgctcattatttcctgatgacattgtatgcagATAAACTTGAGGTCTCCTCAAACAAATTCGGCATTTCAGAAACTCTTTGGACTTCCACCAGAGGAATTTCTCATCAATGATTTTACTTGTCACTTGAAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcctttttcgccatcacttgttctatttctataatgacagaacaaatcatgcagATAAATTTGCGGTCTGCCCAAACAAATGCAGCATTTCGGAAACTCTTTAACCTCCCACCGGAAGAGTTTCTCATCGATGATTTTACCTGCCATCTAAAAC
ttctatttctataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcgaattgagcagctcttttgttggcctttttcgccatcacttgttctatttctataatgacagaacaaatcatgcagATAAATTTGCGGTCTGCCCAAACAAATGCAGCATTTCGGAAACTCTTTAACCTCCCACCGGAAGAGTTTCTCATCGATGATTTTACCTGCCATCTAAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA