Sequence
atgc intronic sequence ATGC exonic sequencegtatgaagccagaaccttttcgttatgcttcaaaacctaactggtacgtgtttacttttgaagctcatcaagttcatcttttttgttggttagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g43374.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G173137_T01 (Zea mays), 3'ss of exon 8
gtatgaagccagaaccttttcgttatgcttcaaaacctaa--ctggtacgtgtttacttttgaagctcatcaagttcatcttttttgttggttagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
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-------------------gtattatgtcctcaagtttaaaactattgccctgttatttctgaagctcatcgattttatgttttcatctggttagCGGTTTGGAAGTGGTTCAATACCAACACATCTTGTTGGGGCTGCTTTGCTTAGAGGAGAGTGGAAGGTTGCTGTAAACTTGATTCTTGATCCAAGGGAAG
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G427822_T01 (Zea mays), 3'ss of exon 7
gtatgaagccagaaccttttcgttatgcttcaaaacctaa--ctggtacgtgtttacttttgaagctcatcaagttcatcttttttgttggttagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
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-------------------gtattatatcctcaagtttaaaactattgccctgttatttctgaagctcatcgattttatcttttcatctggttagCAGTTTGGAAGTGGTTCAATACCAACACATCTTGTTGGGGCTGCTTTGCTTAGAGGAGAGTGGAAGGTTGCTGTAAACTTGATTCTTGATCCAAGGGAAG
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G307981_T01 (Zea mays), 3'ss of exon 5
gtatgaagccagaaccttttcgttatgcttcaaaacctaactggtacgtgtttactttt------gaagctcatcaagttcatcttttttgttggttagCGTTTTGGAAGTGGT--TCAGTACCTACTCACCTTGTTGGAGC-TGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG-----
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------gggctgctttgcttagaggagagtggaaggttgctgtaaacttgattcttgatccaagggaaggagatatcctacaaatattttatatgtgtccaattagGAGTTTGTATTCAGTCTTGCCAGCTTTTGTTTAAACATAACTAAGTTCGTACAGCGTGATGACAT-CAATGAATTGCGCAAACATTACAAAGAACATGGTG
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 9
---------gtatgaagccagaaccttttcgttatgcttcaaaacctaactggtacgtgtttacttttgaagctcatcaagttcatcttttttgttggttagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
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cttgagagtgaatcaggcctaattcatttctaatagactgattattttaacatttttttttcatttttgc--tttatgagcaactaatttgtatgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCAAGGGGAATGGAAACTTGCTGTAGACATGATCCTTGATCCAAGAGATG
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G43270.1 (Glycine max), 3'ss of exon 9
--------gtatgaagccagaaccttttcgttatgcttcaaaacctaactggtacgtgtttacttttgaagctcatcaagttcatcttttttgttggttagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
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gttcatttctattagactgattattttaagacttaattttatttttcatttatgctttacaagcaactaatttgtatgtgaatgtgctcactgt-gctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCGAGGGGAATGGAAACTTGCTGTAGACATGATCCTCGATCCAAGAGATG
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G04820.1 (Arabidopsis thaliana), 3'ss of exon 9
----------------------------------------------------------------gtatgaagccagaaccttttcgttatgcttcaaaacctaactggtacgtgtttacttttgaagctcatcaagttcatctttt--ttgttggttagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
|| | | || ||| | || || | | ||| | | | | | | || | || | || || | |||| | ||||||||||||||||||||||||| || |||| ||| |||||||| | | | ||||||||||| | | ||||| | |||||||||||||||| |||
gtactattctcttgtcgagttgtaatgatatatatgttattttctctttttagtttttagtagctaattcaacttacacttttgcattgtggtatcgagtagtacttgaatattatcaaatagaaatattttcttatgaattttgtaattgtgtgacagCGTTTTGGAAGTGGTTCAGTACCAACCCACCATGTAGGAGCTGCACTATTGAAAGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAA
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 4
gtatgaagccagaaccttttcgttatgcttcaaaacctaactggtacgtgtttacttttgaagctcatcaagttcatcttttttg------ttggt-tagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
| | | || | |||| || | | || | || | | | | ||| || | || || | ||| | ||||||||||||||||||| || || ||||||||| |||||||||| || || |||||||||||| || | |||| | |||||||| |||||||| ||||
gctttcttctgttacaccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaatttaactcattggaacaaattgctgcagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactggtacgtgtttacttttgaagctcatcaagttcatcttttttgttggttagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
acctaac putative branch site (score: 2)
ttcatcttttttgtt putative PPT
tttactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaagccagaaccttttcgttatgcttcaaaacctaactggtacgtgtttacttttgaagctcatcaagttcatcttttttgttggttagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT