Sequence
atgc intronic sequence ATGC exonic sequencegtagtgatacatcgtgttcattgtcatttatttcatcgccgaaatgggcatgacataatccattcctggacctgcattgacagacatacattctttcatcctgtgaaatgaacgaattccatcagGGTTCAACGTGGAGAAGGTGGAGTACAAGAACGTGGCCTTCACGGTGTGGGACGTGGGAGGCCAGGACAAGCTCCGACCTCTCTGGAGACAATACTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g02390.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g02390.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G058474_T01 (Zea mays), 3'ss of exon 2
gtagtgatacatcgtgttcattgtcatttatttcatcgccgaaatgggcatgacataatccattcctggacctgcattgacagacatacattctttcatcctgtgaaatgaacgaattccatcagGGTTCAACGTGGAGAAGGTGGAGTACAAGAACGTGGCCTTCACGGTGTGGGACGTGGGAGGCCAGGACAAGCTCCGACCTCTCTGGAGACAATACTTCAG
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---------------------------gtatg-cgtctctcatagagctacg--ttgatcctcgtagtagaccacggttcgaggta-gcattgtgtgtgtgtgtg---tgtgtgtgtgtgtgcagGTTTCAACGTGGAGAAAGTTGAGTACAAGAACGTGGCCTTCACGGTGTGGGACGTCGGAGGGCAGGACAAGCTGCGGCCGCTGTGGAGGCAGTACTTGAG
upper sequence: LOC_Os06g02390.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EDP05355 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtagtgatacatcgtgttcattgtcatttatttcatcgccgaaatgggcatgacataatccattcctggacctgcattgacagacatacattctttcatcctgtgaaatgaacgaattccatcagGGTTCAACGTGGAGAAGGTGGAGTACAAGAACGTGGCCTTCACGGTGTGGGACGTGGGAGGCCAGGACAAGCTCCGACCTCTCTGGAGACAATACTTCAG
||| | || | || | | | | | ||| ||||| || || || | || ||| | | | |||| || || |||| |||||||| ||||||||| | ||||||||||| | |||||||||||||||||||| |||||||| ||||| || || || ||| | || |||||||
----cccagtatcccagcccatgc--tccatgtaccccttattacagcccgaacagaatcc---cccacacacacaat-----ccacacacacctgcgccctgcaaaccga-----------cagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGGACGTGGGCGGCCAGGAGAAGCTGCGGCCACTGTGGCGGCATTACTTCAA
upper sequence: LOC_Os06g02390.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ08154 (Selaginella moellendorffii), 3'ss of exon 2
gtagtgatacatcgtgttcattgtcatttatttcatcgccgaaatgggcatgacataatccattcctggacctgcattgacagacatacattctttcatcctgtgaaatgaacgaattcc-atcagGGTTCAACGTGGAGAAGGTGGAGTACAAGAACGTGGCCTTCACGGTGTGGGACGTGGGAGGCCAGGACAAGCTCCGACCTCTCTGGAGACAATACTTCAG
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------------------------------------------------------gtaatcctttttttctggtttcttggctttcatcttggccttcttgct-cgactgatgtgaatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTGGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
upper sequence: LOC_Os06g02390.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
gtagtgatacatcgtgttcattgtcatttatttcatcgccgaaatgggcatgacataatcca-ttcctggacctgcattgacagacatacattctttcatcctgtgaaatgaacgaattcc-atcagGGTTCAACGTGGAGAAGGTGGAGTACAAGAACGTGGCCTTCACGGTGTGGGACGTGGGAGGCCAGGACAAGCTCCGACCTCTCTGGAGACAATACTTCAG
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----------------------------------------------gtaatccttttttctggtttcttggctttcatc--ttgaccttc-ttgctcgatttctcgactgatgtgaatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgcattgacagacatacattctttcatcctgtgaaatgaacgaattccatcagGGTTCAACGTGGAGAAGGTGGAGTACAAGAACGTGGCCTTCACGGTGTGGGACGTGGGAGGCCAGGACAAGCTCCGACCTCTCTGGAGACAATACTTCAG
cattgac putative branch site (score: 3)
ttccatc putative PPT
atacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtgatacatcgtgttcattgtcatttatttcatcgccgaaatgggcatgacataatccattcctggacctgcattgacagacatacattctttcatcctgtgaaatgaacgaattccatcagGGTTCAACGTGGAGAAGGTGGAGTACAAGAACGTGGCCTTCACGGTGTGGGACGTGGGAGGCCAGGACAAGCTCCGACCTCTCTGGAGACAATACTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA