Sequence
atgc intronic sequence ATGC exonic sequence...atatgtttttagcttctgaaacaagtcatgcattttagctttattttgattaattattcattattgtcaagctattaatttgtcctgaccttttatccagGTCAACAATATCAGTGGTTATCTCCCTGGAAGGATTGTCTTTTTCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g07130.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 14
---atatgtttttagcttctgaaacaagtcatgcattttagctttattttgattaattattcattattgtcaagctattaatttgtcctgaccttttatccagGTCAACAATATCAGTGGTTATCTCCCTGGAAGGATTGTCTTTTTCTTG
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actatttgctataatatgctttcagtttttgaatcttgagattctgtcttgtttagtgtttcttcatttgaaagttat--actt-ttctgaccttgtacccagGTAAATAATATCAGCGGTTATCTCCCTGGGAGGATTGTCTTCTTCTTG
upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 20
atatgtttttagcttctgaa-acaagtcatgcattttagctttat---tttgatt--aattattcattattgtcaagctattaatttgtcctgaccttttatccagGTCAACAATATCAGTGGTTATCTCCCTGGAAGGATTGTCTTTTTCTTG
| | || ||| ||| | | ||| ||| || ||| || || | | |||| || || ||||| | ||| | ||| || |||| |||||||||||||| || || |||||| | |||||||||||||||
-----tgtagagtacctgtgtgtgtgtccttgaattttgctctacccatttagtttcaagtgactttgattgctaa-ctgttaatagcttctgtcttttggtctagGTGAACAATATCAGTGGCTACCTTCCTGGACGAATTGTCTTTTTCTTG
upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 15
atatgtttttagcttctgaaacaagtcatgcattttagctttat---tttgatt--aattattcattattgtcaagctattaatttgtcctgaccttttatccagGTCAACAATATCAGTGGTTATCTCCCTGGAAGGATTGTCTTTTTCTTG
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-tagagtacctgtgtgtg---tgtgtccttgaattttgctctacccatttagtttcaagtgactttgattgctaa-ttgttaatagcttctgtcttttggtctagGTGAACAATATCAGTGGTTACCTTCCTGGACGAATTGTCTTTTTCTTG
upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 14
atatgtttttagcttc--tgaaacaagtcatgcattttagctttattttgattaattattcattattgtcaagctattaatttgtcctgaccttttatccagGTCAACAATATCAGTGGTTATCTCCCTGGAAGGATTGTCTTTTTCTTG
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-ta-atcattggattcagcggattcagatgtaataatctgattgatctatagtgtgttcctttaattttgtatttactcagtagcgttatctattgtttcagGTCAACAATATCAGTGGCTATCTTCCTGGGCGGATTGTGTTTTTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattaattattcattattgtcaagctattaatttgtcctgaccttttatccagGTCAACAATATCAGTGGTTATCTCCCTGGAAGGATTGTCTTTTTCTTG
tcctgac putative branch site (score: 2)
ccttttatcc CT-rich tract
taattattcattattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatgtttttagcttctgaaacaagtcatgcattttagctttattttgattaattattcattattgtcaagctattaatttgtcctgaccttttatccagGTCAACAATATCAGTGGTTATCTCCCTGGAAGGATTGTCTTTTTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - -gcttctg
- - - - - - - - - aaacaag
- - - - - - - - - - - - -tcatgca