Sequence
atgc intronic sequence ATGC exonic sequence...ccgtcatgatctatcttatgaaaagaagtgacagtgacttgatctgccttatcaatggcataattttttgacatattattaacatatctggccttgacagGTTGCAATCAAGAAAATGAAGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g02555.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G864414_T02 (Zea mays), 3'ss of exon 5
-------------------ccgtcatgatctatcttatgaaaagaagt-----gacagtgacttgatctgccttatcaatggcataattttttgacatattattaacatatctggccttgacagGTTGCAATCAAGAAAATGAAGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG
| | | | | ||| | | | ||| || | ||| | || | || |||| || ||||||| ||| |||| || || ||||||| |||||||| ||||||||||| |||||||| ||||| |||||||| || |||||||||||||||
gtatgtcattaggcttgcccatttgttgcttgtgttacaccttaacttttttcaatagttacacagttcag-ttacccattgt-tagcctttt--caccttattaagatacctgggct-gatagGTTGCGATCAAGAAGATGAAGAAAAAGTATTATTCTTGGGAAGAGTGCATAAACCTCCGTGAAGTGAAG
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G08080.1 (Glycine max), 3'ss of exon 2
ccgtcatgatctatcttatgaaaagaagtgacagtgacttgatctgccttatcaatggcataattttttgacatattattaacatatctggccttgacagGTTGCAATCAAGAAAATGAAGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG
|| | || ||| | | || || | ||||| | | ||| | || | |||||||||||||||||||||||| || |||||||| || ||||||||||| | || || | ||||| |||
---------------------------gtaagtatgttttgggtcgaatgatacgtgaagttgcattttgtattttctctaatttgtcctaatattacagGTTGCAATCAAGAAAATGAAAAAGAAATATTACTCTTGGGAGGAGTGTGTAAACCTGAGAGAAGTCAAG
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 2
ccgtcatgatctatcttatgaaaagaagtgacagtgacttgatctgccttatcaatggcataattttttg-acatattat-taacatatctggccttgacagGTTGCAATCAAGAAAATGAAGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG
|| | || | || | | || | | | || || | || | ||| | || | |||||||||||||||||||||||| || |||||||| || ||||||||||| | || || | ||||| |||
---------------------------gtaagtatgtttagagtagaatgatacgcgaagttacattgtgtgtgttttctctaatttgtcctaatattacagGTTGCAATCAAGAAAATGAAAAAGAAATATTACTCTTGGGAGGAGTGTGTAAACCTGAGAGAAGTCAAG
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G35190.1 (Glycine max), 3'ss of exon 2
ccgtcatgatctatcttatgaaaagaagtgacagtgacttgatctgccttatcaatggcataattttttgacatattattaacatatctggccttgacagGTTGCAATCAAGAAAATGAAGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG
| | ||| | | || || ||| | | |||| || | | | || | | | | || || ||| | | | |||||||| ||||||||||||||||| |||||||| || ||||||||||| | || || | ||||| |||
-----gtaag-tatgct-ttaactgacatgataaaggt---atctctatttcaagttggatgttgtcctaa-atcctaataagttgtaaaa---ttgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTAAACCTGAGAGAAGTCAAG
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G34610.1 (Glycine max), 3'ss of exon 2
ccgtcatgatctatcttatgaaaagaagtgacagtgacttgatctgccttatcaatggcataattttttgacatattattaacatatctggccttgacagGTTGCAATCAAGAAAATGAAGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG
|| | | | ||| | | ||| ||| || || | | | || | | | | || || ||| | | | |||||||| ||||||||||||||||| |||||||| || ||||||||||| | || || | ||||| |||
--gtaa--gtatgctttaattgacataatgaaggtggctctattt------caagttagatgttgtcctaa-atcctaataagttgttaaa---ttgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTAAACCTGAGAGAAGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccttatcaatggcataattttttgacatattattaacatatctggccttgacagGTTGCAATCAAGAAAATGAAGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG
tattaac putative branch site (score: 1)
ataattttttgacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccgtcatgatctatcttatgaaaagaagtgacagtgacttgatctgccttatcaatggcataattttttgacatattattaacatatctggccttgacagGTTGCAATCAAGAAAATGAAGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG