Sequence
atgc intronic sequence ATGC exonic sequencegtgagtactgcacattcagtcaggagttagcatgagcccatgaatcatcgttatcacgggaaaagttactcatgttaaccccatcctctttgccagGTTCTCCAGGCAATCCGGTTACACCTGTTGGTGGCTGCCGATATGATAGCTCCCTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g06200.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G829408_T01 (Zea mays), 3'ss of exon 4
gtgagtactgc-acattcagtcaggagttagcatgagcccatgaatcatcgttatcacgggaaaagttactcatgttaacccca--tcctctttgccagGTTCTCCAGGCAATCCGGTTACACCTGTTGGTGGCTGCCGATATGATAGCTCCCTAG
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gtgagtgatgccacacttg---------taatgtaaacc-ataaatcatc-ctatttgggtccaa--tactcaattcaattgcaaatactcttcctcagGTTCTCCAGGCAATCTTTCTACTCCTGTTGGTGGCTGCCGCTATGATAGCTCCCTCG
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G052515_T01 (Zea mays), 3'ss of exon 2
gtgagtactgc-acattcagtcaggagttagcatgagcccatgaatcatcgttatcacgggaaaagttactcatgttaacccca--tcctctttgccagGTTCTCCAGGCAATCCGGTTACACCTGTTGGTGGCTGCCGATATGATAGCTCCCTAG
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gtgagtgatgccacacttg---------taatgtaaacc-ataaatcatc-ctatttgggaccaa--tactcaattcaattgcaaatactcttcctcagGTTCTCCGGGCAATCCTTCTACTCCTGTTGGTGGCTGCCGCTATGATAGCTCCCTCG
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G029735_T01 (Zea mays), 3'ss of exon 1
gtgagtactgc-acattcagtcaggagttagcatgagcccatgaatcatcgttatcacgggaaaagttactcatgttaacccca--tcctctttgccagGTTCTCCAGGCAATCCGGTTACACCTGTTGGTGGCTGCCGATATGATAGCTCCCTAG
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gtgagtgatgccacacttg---------taatgtaaacc-ataaatcatc-ctatttgggaccaa--tactcaattcaattgcaaatactcttcctcagGTTCTCCGGGCAATCCTTCTACTCCTATTGGTGGCTGCCGCTATGATAGCTCCCTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatcatcgttatcacgggaaaagttactcatgttaaccccatcctctttgccagGTTCTCCAGGCAATCCGGTTACACCTGTTGGTGGCTGCCGATATGATAGCTCCCTAG
tgttaac putative branch site (score: 2)
ccccatcctctttgcc CT-rich tract
aaaagtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtactgcacattcagtcaggagttagcatgagcccatgaatcatcgttatcacgggaaaagttactcatgttaaccccatcctctttgccagGTTCTCCAGGCAATCCGGTTACACCTGTTGGTGGCTGCCGATATGATAGCTCCCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG