Sequence
atgc intronic sequence ATGC exonic sequence...tctagctctatattgcaaatgtacaaaatatgttttgtgtgacatacagataatcaatcaatctatcagttattcataatcatattttggactatttcagATACTTCACTGGTCTCTTGTCACCATGGAAAGGCATTTTACTTTTTGGTCCCCCAGGAACTGGGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g55260.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 5
tctagctctatat-tgcaaatgtacaaaatatgttttgtgtgacatacagataatcaatcaatctatcagttattcataatcatatt--ttggactattt-cagATACTTCACTGGTCTCTTGTCACCATGGAAAGGCATTTTACTTTTTGGTCCCCCAGGAACTGGGAAG
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--taataatatggatacaaatataca--atgctaggcatatgaatgagtgccaatctttctactttttcactaattctatgtgtactgtttgtgctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG
upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 5
tctagctctatattgcaa-atgtacaa--aatatgttttgtgtgacatacagataat-caatcaatctatcagttattcataatcatattttggactatttc-agATACTTCACTGGTCTCTTGTCACCATGGAAAGGCATTTTACTTTTTGGTCCCCCAGGAACTGGGAAG
|| | ||| || || ||| | || | | | | | | ||||||| | | || ||| || |||| | | | || || || ||||| |||||||| | |||||||||||||| ||| | ||||||||||| |||||||| || |||
-----ttcatttttggaagatttactatgaacacatgacgaattgcccaaagataatgctttgaaatcttcatttcacaataagctgacctatcccttcatctagGTACTTTACTGGTCTTCTATCACCATGGAAAGGTATTCTCCTTTTTGGTCCTCCAGGAACAGGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagataatcaatcaatctatcagttattcataatcatattttggactatttcagATACTTCACTGGTCTCTTGTCACCATGGAAAGGCATTTTACTTTTTGGTCCCCCAGGAACTGGGAAG
ctatttc CT-rich tract
agttattcataatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctagctctatattgcaaatgtacaaaatatgttttgtgtgacatacagataatcaatcaatctatcagttattcataatcatattttggactatttcagATACTTCACTGGTCTCTTGTCACCATGGAAAGGCATTTTACTTTTTGGTCCCCCAGGAACTGGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA