Sequence
atgc intronic sequence ATGC exonic sequencegtttattgtgcttgtccattgtcttgttctgtttcattaatgtacatgttgtcttttacagAATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g56646.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
----------------gtttattgtgcttgtccattgtcttgttctgtttcattaatgtacatgttgtcttttacagAATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCG
| || | | || | |||| || || | ||||| | ||||| | || ||||||||||| || ||| ||||| ||||| ||||| ||||||||||||| |||| ||||| || || ||||||||||| |
gtatgtctgggggatgagatgctggagtgtttcacttgcttgctcagtgt--ttaatatttttgttgcccttcccagAATGCTACACAGAAA-AGTCAGAAGGTATTTGTCCATGTTCCTTCAG-AAATTGCTGCTCATGAAGTTGAGGAAATTG
upper sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 4
---------------gtttattgtgcttgtccattgtcttgttctgtttcattaatgtacatgttgtcttttacagAATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCG
|| || || | || | |||| || || | ||||| | | || || |||||||||||| ||||| ||| ||||| ||||| ||||| ||||||||||||| |||| || || || || ||||||||||| |
gtacataacttgctgagttgctggagtttttcacttgcttgctcagtgt--ttaatttg--ttttttcctttacagAATGCAACTCAGAAA-AGTCAGAAGGTATTTGTCCATGTTCCTTCAG-AAATTGCAGCTCATGAAGTTGAGGAAATTG
upper sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------------------------gtttattgtgcttgtccattgtcttgttctgtttca------ttaatgtacatgttgtcttt--tacagAATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCG
| | ||| ||| || || ||| |||| || | || | | |||||||||| ||||||||| |||||||| |||||||| ||||| || |||| | || ||||| || || ||||||||||| |
gtacaaattaagtccgtcatatctttgatagaaatcttatatatctgttcttgctgatattttgcaaaagtaatcctgctgtatgtgatggtgggacgggagctagtgtttgctcaacactaaattagtactcaaagaaactaatatatagtttattctgagtacagAATGCCACTCAAAAA-AGTCAAAAAGTGTTTGTGCATGTGCCATCAG-AGATTGCTGCTCATGAAGTTGAGGAAATAG
upper sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------------------------------------gtttattgtgcttgtccattgtcttgttctgtttca------ttaatgtacatgttgtctttt--acagAATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCG
| | ||| ||| || || |||| | | || | || | | | ||||||||| ||||||||| ||||||||||||||||| ||||| || |||| | || ||||| || || |||||||||||
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttattttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAA-AGTCAAAAGGTGTTTGTGCATGTGCCATCAG-AGATTGCTGCTCATGAAGTTGAGGAAATA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgcttgtccattgtcttgttctgtttcattaatgtacatgttgtcttttacagAATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCG
cattaat putative branch site (score: 3)
ttgtctttt putative PPT
tttcattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttattgtgcttgtccattgtcttgttctgtttcattaatgtacatgttgtcttttacagAATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC