Sequence
atgc intronic sequence ATGC exonic sequence...gatcaaaaccatttttgtgacattgtcaaatcttgaacaaactgcttgcactttatggagaacagaatgtgacataaatagtcaataaattgtcacacagGAAAGTCATGAGGAAGCTGCAGAGGAGTTACCAAGCAAAGTTAAGTTTTTCTTCAGTGCAGCAATTGAAGCTTGGGACGCAGAGTTCTATGTGAAAGTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g07905.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g07905.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G000393_T02 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------------gatcaaaaccatttttgtgacattgtcaaatcttgaacaaactgcttgc-actttatggagaacagaatgtgacat--aaatagtcaataaattg--tcacacagGAAAGTCATGAGGAAGCTGCAGAGGAGTTACCAAGCAAAGTTAAGTTTTTCTTCAGTGCAGCAATTGAAGCTTGGGACGCAGAGTTCTATGTGAAAGTCG
| | ||| || ||| | ||||| | | | || | ||| | || | || | ||||||| | | ||| | |||||||||||||| || |||||||| || ||||| ||||||| || ||||||||||||| ||| ||||||| ||||| |
gtaaggacctattagtacctcttattctcgattgtccttcacaagttgtagtacgcaagcaagacttttgagtttagacctttcttgcttc--catcaaagactaggtaggacccatgtgatcctatacatttcatcaatgaactttgaaatagTAAGCATTTTGGATTGGGCAGGAAAGTCATGAAGAGGCTGCAGAAGAATTACCGAGCAAAGCAAAAATTTTCTTCAGTGCTGCAGTTGAAGCCTGGGATG---------------------
upper sequence: LOC_Os06g07905.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G000393_T01 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------------gatcaaaaccatttttgtgacattgtcaaatcttgaacaaactgcttgc-actttatggagaacagaatgtgacat--aaatagtcaataaattg--tcacacagGAAAGTCATGAGGAAGCTGCAGAGGAGTTACCAAGCAAAGTTAAGTTTTTCTTCAGTGCAGCAATTGAAGCTTGGGACGCAGAGTTCTATGTGAAAGTCG
| | ||| || ||| | ||||| | | | || | ||| | || | || | ||||||| | | ||| | |||||||||||||| || |||||||| || ||||| ||||||| || ||||||||||||| ||| ||||||| ||||| ||||| || ||||| ||||| |
gtaaggacctattagtacctcttattctcgattgtccttcacaagttgtagtacgcaagcaagacttttgagtttagacctttcttgcttc--catcaaagactaggtaggacccatgtgatcctatacatttcatcaatgaactttgaaatagtaagcattttggattgggcagGAAAGTCATGAAGAGGCTGCAGAAGAATTACCGAGCAAAGCAAAAATTTTCTTCAGTGCTGCAGTTGAAGCCTGGGATGCAGAATTTTATGTCAAAGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcactttatggagaacagaatgtgacataaatagtcaataaattgtcacacagGAAAGTCATGAGGAAGCTGCAGAGGAGTTACCAAGCAAAGTTAAGTTTTTCTTCAGTGCAGCAATTGAAGCTTGGGACGCAGAGTTCTATGTGAAAGTCG
ataaatagtcaataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatcaaaaccatttttgtgacattgtcaaatcttgaacaaactgcttgcactttatggagaacagaatgtgacataaatagtcaataaattgtcacacagGAAAGTCATGAGGAAGCTGCAGAGGAGTTACCAAGCAAAGTTAAGTTTTTCTTCAGTGCAGCAATTGAAGCTTGGGACGCAGAGTTCTATGTGAAAGTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC