Sequence
atgc intronic sequence ATGC exonic sequencegtgatctcttgcaattttttagaacattgtatcaacttccatcatgatagtgtatcgagttttactttaagccatatatccactgagtgatttgcatattattaccttcacttgatttcttaatagGTTAAGAAAACTGGGATGCCACCTGGCCCCAGAGCTGGGTTTTCTATGTGCGTTCACAAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g40740.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g40740.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 7
gtgatctcttgcaattttttagaacattgtatcaacttccatcatgatagtgtatcgagttttactttaa--gccatatatcc--actgagtgatttgcatatt-attaccttcacttgatttcttaatagGTTAAGAAAACTGGGATGCCACCTGGCCCCAGAGCTGGGTTTTCTATGTGCGTTCACAAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAAA
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-------------------------------aggaattttatattgacaacattttgagttttgccttaaaagctacaggtccccatctagtgttttttatatttactttgttaatcttaattgctaatagGTTAAGAAGGCTGGGATGCCGCCTGGTCCCAGAGCTGGTTTTTCAATGTGTGTGCACAAGAAAAGGGCTGTTCTTTTTGGTGGTGTGGTAGATATGGAAG
upper sequence: LOC_Os04g40740.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 10
gtgatctcttgcaattttttagaacattgtatcaacttccatcatgatagtgtatcgagttttactttaagccatatatccactgagtgatttgcatattattaccttcacttgatttcttaatagGTTAAGAAAACTGGGATGCCACCTGGCCCCAGAGCTGGGTTTTCTATGTGCGTTCACAAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAAA
| ||| | || || | ||| | | | | || || || | ||| | || | |||| | |||| ||| | || || | ||| | | |||||||||||| ||| ||||| ||||| || | ||||||||||| ||||| ||||| |||| ||||||| | || || |||||||| || ||||| |||
---------tacaact----gaaaaataggctcatacacactgaaaaccatgcattttattatctttt------tgta-caactggtttattttcatcatcttttctcc------cttcatgacagGTTAAGAAAAGTGGAATGCCTCCTGGTCCTCGTGCTGGGTTTTCCATGTGTGTTCATAAGAGAAGGGCTCTGCTATTTGGTGGTGTTGTGGATATAGAAG
upper sequence: LOC_Os04g40740.4 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 10
gtgatctcttgcaattttttagaacattgtatcaacttccatcatgatagtgtatcgagttttactttaagccatatatccac-tgagtgatttgcatattattaccttc-acttgatttcttaatagGTTAAGAAAACTGGGATGCCACCTGGCCCCAGAGCTGGGTTTTCTATGTGCGTTCACAAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAAA
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-----------------------aattaatgctaagtaac-taaaaatttttgaccg--ccctacttc--tccatcaaagagcatgcctgatgtctatgtttctacttctgattttcctttctaatagGTGAAGAAATCTGGGATGCCTCCTGGACCTCGTGCTGGGTTTTCTATGTGTGTCCATAAAAAAAGGGCTGTGCTATTTGGGGGTGTAGTTGATATGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatatatccactgagtgatttgcatattattaccttcacttgatttcttaatagGTTAAGAAAACTGGGATGCCACCTGGCCCCAGAGCTGGGTTTTCTATGTGCGTTCACAAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAAA
acttgat putative branch site (score: 5)
tttctt CT-rich tract
atttgcatattatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatctcttgcaattttttagaacattgtatcaacttccatcatgatagtgtatcgagttttactttaagccatatatccactgagtgatttgcatattattaccttcacttgatttcttaatagGTTAAGAAAACTGGGATGCCACCTGGCCCCAGAGCTGGGTTTTCTATGTGCGTTCACAAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT