Sequence
atgc intronic sequence ATGC exonic sequencegtttttcctataaccctctaagttacattgcgtgcagtttttgattatcatctatatgtttatgattggggaatatacttaacatcttatattctcaagtgcagTTTGCTTGCCTTATCACCTGATGATGTGCTACCTGCTGTTTATTTATGTACTAATAAAATTTCTCCTGACCATGAAAATATT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g49180.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g49180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G53000.1 (Glycine max), 3'ss of exon 1
-----------------------------gtttttcctataaccctctaagttacattgcgtgcagtttttgattatcatctatatgtttatgattggggaatatacttaacatcttatattctcaa-gtgcagTTTGCTTGCCTTATCACCTGATGATGTGCTACCTGCTGTTTATTTATGTACTAATAAAATTTCTCCTGACCATGAAAATATT
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gttcctttgttactaatcacactctttgtgttatccatttcctccctctttttttattgaatagtgaaactgtttttc--ccgtaattggctgattgaggaacattatttgcatgcaatgtttctatcacatagTTTGTTGGCCTTATCTCCAGCAGATGTGCTTCCTGCTGTGTATCTATGCACTAACAAAATTGCTGCAGACCATGAAAATAAG
upper sequence: LOC_Os01g49180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0006g02190.t01 (Vitis vinifera), 3'ss of exon 2
--------------------gtttttcctataaccctctaag---------ttacattgc-gtgcag------tttttgattatcatcta------tatgttta---tgattggggaatatacttaacatcttatatt-ctca-agtgcagTTTGCTTGCCTTATCACCTGATGATGTGCTACCTGCTGTTTATTTATGTACTAATAAAATTTCTCCTGACCATGAAAATATT
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gtttgttgatgttgattgcacttttttgtttcatcctttaaaagaaaaatatttccttgctatgaaaacttgtttttagaagaggatgcactgtattatacctggacttattggggcatgctgtttgcttgcaatgtttctcatggcacagTTTGTTGGCCTTGTCTCCTGAGGATGTGATACCTGCTGTATATCTCTGCACAAATAAGATTGCTGCTGACCATGAAAATATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctatatgtttatgattggggaatatacttaacatcttatattctcaagtgcagTTTGCTTGCCTTATCACCTGATGATGTGCTACCTGCTGTTTATTTATGTACTAATAAAATTTCTCCTGACCATGAAAATATT
acttaac putative branch site (score: 3)
tattctc putative PPT
aatatacttaacatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttcctataaccctctaagttacattgcgtgcagtttttgattatcatctatatgtttatgattggggaatatacttaacatcttatattctcaagtgcagTTTGCTTGCCTTATCACCTGATGATGTGCTACCTGCTGTTTATTTATGTACTAATAAAATTTCTCCTGACCATGAAAATATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT