Sequence
atgc intronic sequence ATGC exonic sequencegtatttctttcagtacaaagtcacaaggctaccttttcctccctttctgttgtttttaacagcacttttgtttccttacttttcatacacagAGGAGTACATTGGTTTAGATGATAACAAATATATTGGTGACCTCCTATCTGAATTCAAGGCAGCCAAGGATCGGAACAAAGGAGAAATTTTACACTGCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g57140.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------gtatttctttcagtacaaagtcacaaggctaccttttcctccctttctgttg--tttttaacagcacttt-tgtttccttacttttcatacacagAGGAGTACATTGGTTTAGATGATAACAAATATATTGGTGACCTCCTATCTGAATTCAAGGCAGCCAAGGATCGGAACAAAGGAGAAATTTTACACTGCAA
|| || | | || || ||| || | || | ||| | | ||| | |||| ||| ||| ||| ||||||| |||||||| ||||||||||||||||||||||||||| | |||||||||||||| |||| |||||||| ||||||||||||||| | || |||||
gtaattaccaatccatattgttttttcttttctatttcttaatttaattaatgcatgtggtttggatatcatggag-caggaggaaacataggtggattttgtagaaaaatttcaagtaacacggtgcatttctttatcttttatatgcagAGGAATACATTGGATTAGATGATAACAAATATATTGGTGACTTGCTATCTGAATTCAAATCAGCTAAGGATCGCAACAAAGGAGAAATTCTTCATTGCAA
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------------------gtatttctttcagtacaaagt-cacaaggctaccttttcctccctttctgttgttttt--aacagcacttttgtttccttacttttcatacacagAGGAGTACATTGGTTTAGATGATAACAAATATATTGGTGACCTCCTATCTGAATTCAAGGCAGCCAAGGATCGGAACAAAGGAGAAATTTTACACTGCAA
| | || | ||| | || || | | | || || | ||||||| | | || | |||| ||| ||| ||| ||||||| |||||||| ||||||||||||||||||||||||||| | ||||||||||||| |||| |||||||| ||||||||||||||| | || |||||
gtaactagcaagtcatattctttttttcccttttctatttcataatttaaataatcctccatgtggtttggatatcaaggagcagaaagaaatgtattaggattttgtagatgtttttcaagtaacatgtgcttttctttatcttttatatgcagAGGAATACATTGGATTAGATGATAACAAATATATTGGTGACTTGCTATCTGAATTCAGATCAGCTAAGGATCGCAACAAAGGAGAAATTCTTCATTGCAA
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 10
gtatttctttcagtacaaagtcacaaggctaccttttcctccctttctgttgtttttaacagcacttttgtttccttacttttcatacacagAGGAGTACATTGGTTTAGATGATAACAAATATATTGGTGACCTCCTATCTGAATTCAAGGCAGCCAAGGATCGGAACAAAGGAGAAATTTTACACTGCAA--
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------------------------------------------------------gttaattgtctgacagctccttt--tattgttactaagagGAGTACATTGGGTTAGATGCAAACAAATATATTGGGGATCTCCTGGCAGAATTTAAAGCTGCAAAGGATCGGAGTAAAGGAGAAATCTTGCACTGTAAAC
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 7
gtatttctttcagtacaaagtcacaaggctaccttttcctccctttctgttgtttttaacagcacttttgtttccttacttttcatacacagAGGAGTACATTGGTTTAGATGATAACAAATATATTGGTGACCTCCTATCTGAATTCAAGGCAGCCAAGGATCGGAACAAAGGAGAAATTTTACACTGCAA
|| ||| || | | | | | || || | || | || |||| || | | ||| || | || ||| |||||||||||||||| |||||||| |||||||||||||| || ||||| |||||||| || || |||||||| | |||
gtcttttttcctctccttgttttt---gttatattataatcaaa----gctgaagttaatagtcttacagCTTCTTT--TATTGTTACTCAGAGGAGTACATTGGGTTAGATGAAAACAAATATATTGGGGATCTCCTGGTGGAATTCAAAGCTGCAAAGGATCGAAGTAAA--------------------
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 7
---------------gtatttctttcagtacaaagtcacaaggctaccttttcctccctttctgttgtttttaac-----------agcacttttgtttccttacttttcatacacagAGGAGTACATTGGTTTAGATGATAACAAATATATTGGTGACCTCCTATCTGAATTCAAGGCAGCCAAGGATCGGAACAAAGGAGAAATTTTACACTGCAA-----
| | ||| | || | || | | |||| ||| | | | ||||| || | | | | | |||| ||| |||||||||||||||| ||||||| || ||||||||||| || |||||| | ||||| ||||||| |||||||| | || ||||| || || ||||||||
gttaccggcaccaaatcacctgattctggg-aatggcatgtccttttccactccttgcttgttaatatcgttaacttgctgagatgagtagtctaacagctctttttttgttactcagaggagTACATTGGGCTAGATGACAATAAATATATTGGGGATCTCCTAGCGGAATTTAAGGCAGTGAAGGATCGAAGTAAGGGAGATATATTGCACTGCAAACTAA
upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 6
gtatttctttcagtacaaagtc-acaaggctaccttttcctccctttctgttgtttttaa--cagcacttt--tgtttccttacttttcatacacagAGGAGTACATTGGTTTAGATGATAACAAATATATTGGTGACCTCCTATCTGAATTCAAGGCAGCCAAGGATCGGAACAAAGGAGAAATTTTACACTGCAA
|||| | | | || | | | || || | | | ||| || ||| ||| ||| | || |||| ||||||||| ||||| ||||||||||||||||||||||| || | | | |||||||||||||| |||||| | | |||||||||||||| || |||||
gtatccatcttattatcttctggattattttattttatttttttaaatcagactcactaaattagtcatttgatgtgcactttttctttttacatagAGGAGTATATTGGATTAGATGATAACAAATATATTGGGGATTTATTGGCGGAATTCAAGGCAGCAAAGGATAGAAGTAAAGGAGAAATTTTGCATTGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctccctttctgttgtttttaacagcacttttgtttccttacttttcatacacagAGGAGTACATTGGTTTAGATGATAACAAATATATTGGTGACCTCCTATCTGAATTCAAGGCAGCCAAGGATCGGAACAAAGGAGAAATTTTACACTGCAA
tccttac putative branch site (score: 2)
cacttttgtttcctta CT-rich tract
ttgtttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttctttcagtacaaagtcacaaggctaccttttcctccctttctgttgtttttaacagcacttttgtttccttacttttcatacacagAGGAGTACATTGGTTTAGATGATAACAAATATATTGGTGACCTCCTATCTGAATTCAAGGCAGCCAAGGATCGGAACAAAGGAGAAATTTTACACTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA