Sequence
atgc intronic sequence ATGC exonic sequence...ccagcattttttccctactatttgaccttaattgattactcaccatgttcaacaaagaattgacacccttttgttttgtgaacatgtttcacttttgcagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os03g21680.3 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G398288_T01 (Zea mays), 3'ss of exon 4
ccagcattttttccctactatttgaccttaattgattactcaccatgtt-caacaaagaattgacacccttttgttttgtgaacatgtttcactttt--gcagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
||| || | | | | | | || | | || | | ||| | | | | || || | | | | ||||| | ||| ||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||| |||||
--tccatcttattcttgggaatct-tcatattatgtcacactttaagtttccaagtaacgcgaagacaacagagtctcattaccctgtttaatcttttggcagGGGCAAATGATGTTTCAATGATACAGATGGCTGATGTTGGTGTTGGCATATGTGGTCAAGAAGGTCGTCAGGCAGTGATGGCTTCAGACTTTGCTATGGG
upper sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G41040.1 (Glycine max), 3'ss of exon 8
---------------------------------------------------------------ccagcattttttccctactattt--gaccttaattgattactcaccatg---ttcaaca-aagaattgac---------acccttttgttttgtgaacatgtttcacttttgcagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
| | ||| | | | | | | | | | | | ||| || | | |||| |||| || | |||| | | | | || ||| ||||||| |||||||| |||||||| || ||||||||||||||||| ||||||||||| || ||||| || |||||||||||||||||||||||||| |||||
gtaagatatttgtaatatgaaattgaacttaatttgcatttgggtgttcttgtgaggcctggttgatagtaatttgcatggcagtccaggcttcagatagtgttgccagatggattttgatataagatttgatttaatatgaacttaatcttttttttatctcgattacatttgacagGGGCCAATGATGTGTCAATGATCCAAATGGCAGATGTTGGTGTAGGAATATGTGGGCAGGAAGGGCGCCAAGCAGTGATGGCATCAGATTTTGCTATGGG
upper sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G34610.1 (Glycine max), 3'ss of exon 4
ccagcattttttccctactat--ttgaccttaattgattactcaccatgttcaacaaagaattgacacccttttgttttgtgaacatgtttcacttttg-cagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
| | | ||| | | ||| | | || | | | | ||| | || | | | | || ||| | | ||||| | ||||||||||||||||||||||||| || ||||||||||||||||||||||||||||| || ||||| || |||||||||||||||||||||||||| |||||
cttgtagtttgttatttgtataatcagatgcacttttaaattaagattattccgtatcaaacttatgacgtctt---ctgtttgtttcaattactttggacagGGGCAAATGATGTTTCAATGATCCAAATGGCAGATGTTGGTGTTGGAATATGTGGGCAGGAAGGGCGCCAAGCAGTGATGGCATCAGATTTTGCTATGGG
upper sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G44550.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------------ccagcattttttccctactatttgaccttaattgattactcaccatg---ttcaaca-aagaattgacaccct------tttgttttgtgaacatgtttcacttttg-cagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
|| | ||| | | | | | | | || ||| || | |||| |||| | || | || | | | ||||||| ||||||| ||||| || |||||||| || ||||||||||||||||| || |||||||| || ||||| || |||||||||||||||||||||||||| |||||
gtaagttatttataatatgaaattgcacttaatttgcatttgggtgttgttgtgaggcctggttgatggttgatagtaatttgtatggcagtccaggcttcagctagtgtttccagatggattttgatgtaagatttgatttaatatgaacttaatcttttttgttttgattacttttgacagGGGCCAATGACGTGTCAATGATCCAAATGGCAGATGTTGGTGTAGGGATATGTGGGCAGGAAGGGCGCCAAGCAGTGATGGCATCAGATTTTGCTATGGG
upper sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0058g01400.t01 (Vitis vinifera), 3'ss of exon 4
ccagcattttttccctactatttgaccttaattgattactcaccatgttcaacaaagaattgacacccttttgttttgtgaacatgtttcacttttgcagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
| || | || | | ||| || ||| ||| || | | | | |||| || || | ||| | |||||| || || |||||||||||||| || ||||||||||||||||| |||||||||||||| || || ||||||||||| |||||||| |||||||| |||||
cttgcctgcacaccaccccccctcccctcttctgggtacacacattggttgctaggctggtattgctctttccttcctcttactactgacacctgtgcagGTGCCAACGATGTTTCAATGATTCAAATGGCAGATGTTGGTGTGGGAATATGTGGTCAGGAGGGGCGTCAAGCAGTAATGGCATCGGATTTTGCAATGGG
upper sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
ccagcattttttccctactatttgaccttaattgattactcaccatgttcaacaaa-gaattgacacccttttgttttgtga-acatgtttcacttttg--cagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
| || | | |||| | | | ||| | | ||| | || | | ||| || || ||| | | || ||| |||||||||| || || ||||||||||| ||||| |||||||| ||||| || | || || ||||| || |||||||| ||||| || |||||||| |||||
----ttcgtgttactagtaagttgaagctcttcaaaacttcaggttctcttacatgtgtctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
upper sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ23939 (Selaginella moellendorffii), 3'ss of exon 5
ccagcattttttccctactatttgaccttaattgattactcaccatgttcaacaaagaattgacacccttttgttttgtgaacatgtttcacttttgcagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
| | | |||| | | | | | ||| ||| || ||| | ||| ||| || ||||| || | ||||| |||||||| || || || ||||| ||| | || |||||||| || ||||||||||||||||| |||||||| |||
----------------------------------gtaatcatctttgtttaggagatctcttgaataatttctcttta-----atctttaatcttt--agGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
upper sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ16263 (Selaginella moellendorffii), 3'ss of exon 6
ccagcattttttccctactatttgaccttaattgattactcaccatgttcaacaaagaattgacacccttttgttttgtgaacatgtttcacttttgcagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
| ||| || || || | | | | | |||| || ||| ||| ||| ||| || |||| || |||||||| || |||||||||| ||||||||||| ||||| | |||| || |||||||| |||||||| |||||||| || ||||| ||||
-----------------gtgagtgattttttttcttt--ttgacttttgtggcctagaagtggt----tttcatttcccgaa---gttgtgct----cagGAGCCAATGATGTCTCCATGATACAGACAGCAGATGTTGGAATTGGATTGAGTGGCCAGGAAGGTCGGCAAGCAGTCATGGCATCTGACTTTGCATTGGG
upper sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
ccagcattttttccctactatttgaccttaattgattactcaccatgttcaacaaagaattgacacccttttgttttgtgaacatgtttcacttttgcagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
| | ||| || | || || | | | ||| | | || | | || ||| || ||||| || | ||||| |||||||| || || || ||||| ||| | || |||||||| || ||||||||||||||||| |||||||| |||
--------------------------------------gtaatcatctttgtttaggagtt--ctcttgaataatttctctttaatctttaatctt-tagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttcaacaaagaattgacacccttttgttttgtgaacatgtttcacttttgcagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
aattgac putative branch site (score: 3)
tttcactttt putative PPT
ttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccagcattttttccctactatttgaccttaattgattactcaccatgttcaacaaagaattgacacccttttgttttgtgaacatgtttcacttttgcagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
ccagcat
- - - - - - - - - - - - - - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - -acaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacatgt
