Sequence
atgc intronic sequence ATGC exonic sequencegttagttaagcccaaacaaaccctcattagttaacggttttatgctcagtgttaacttggatgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g47100.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
gttagttaagcccaaacaaaccctcattagttaacggttttatgctc-------------agtgttaacttggatgttggtga--ctgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
|| ||| || | | |||| || | |||| |||| | |||| | | ||| ||||||||| || | | |||||| ||||||||| ||||||||||||||||| ||||||||||||||||||||||| || || |||||||| |||
gtgagtcaaact--aggaaacacttactagtcaacgatgttatacacttcgagaacatcaagtattaacttggctgcttgctgtcctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 7
----------------gttagtta-agcccaaacaaaccctcattagttaacggttttatgctcagtgttaacttgg-----atgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
|| | | || ||||| | | || ||| || | | | || | || | ||| | ||| ||| |||||| ||||| || ||||||||||| ||||||||||| ||||| |||||||| || || ||||||||
tctctgtatgttttatcttgatcacaggttttttaaacc--taccatgaaaataatttgtgataattttttagctgttcaacaaattgctcactcattgcagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGCTAATGGCATACCTTTCCTACATTCTGGCTGAA
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 7
-------------------gttagttaag-cccaaacaaaccctcattagttaacggttttatgctcagtgttaacttggatgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
||| | | | || | ||| | || || || | | | | ||| | ||| ||| |||||| ||||| || ||||||||||| ||||||||||| ||||| |||||||| || || ||||||||
cacttcagtggaatcacttattaactggggtcttcgtaatctaccataaaaaaattgtgataattttttagatgttcaacaaattgctcactcattgcagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGCTAATGGCATACCTTTCCTACATTCTGGCTGAA
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA17G02560.1 (Glycine max), 3'ss of exon 6
----------------------gttagttaagcccaaacaaaccctcattagttaacggttttatgctcagtgttaacttgga----tgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
|| || || || || | | | | | || || | ||| | || |||| || ||||||||||||| |||||||||||||| || ||| | |||||||| ||||||||||||||||| ||||
gttaattctaaattccattacttttgaatatgcttaaccacaacaatgaaatatcccagtacactgttggccattattccctaattcctttactgacaaatcccagGCATTCTACAGACCGTGAGGTTGCTCTCATGGTACTCATGGCATACCTTTCATATATGCTATCTGAA
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 8
----------------------gttagt-taagcccaaacaaaccctcattagttaacggttttatgctcagtgttaacttggatgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
|| || | || | || | | ||| | | ||| | | || || | | | |||||||||| ||||| || ||||||||||| ||||||||| | ||||| ||||| || || ||||| |||||
acaaggttttttagacccgctttttggtatgagacttggcacaggatgatttgaaacaatcttttttactgaggccaaacaaaattctcct---taattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 7
--------------------------gttagttaagcccaaacaaaccctcattagttaacggttttatgctcagtgttaa---cttggatgttg-gtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
|| || || || || | | | || | || || | | ||| ||| || ||| || ||||||||||||| |||||||||||||| || ||| | |||||||| |||||||| ||||||||| |||||
gttaattctaattaagctccattaattttcaatatgcttaaccacatcaatgaaatatatcagtacattgttagctattattcccttattcattttacgacaaatcccagGCATTCTACAGACCGTGAGGTTGCTCTCATGGTACTCATGGCATACCTTTCGTATATGCTGTCTGAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------gttagttaagcccaaacaaaccctcattagttaacggtt-ttatgctcagtgttaacttggatgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
| | ||||| | | || |||| | || |||| || || || | | ||| | | |||||| |||||||| ||||| ||||| ||||||||||| |||||||| | ||||||||| |||| |||
gtatattcgtatctactgatggttaaaaatgtgattttaccctttctttaataatccttttgctttgtttttgttttg-ttttg-----taacatcagGCACTCTACTGATCGTGAAGTTGCACTTATGATGCTATTGGCTTACTTATCATATATGTTGGCAGAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 8
---gttagttaagcccaaaca---aaccctcattagttaa-cggttttatgctcagtgttaacttggatgttg----gtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
|| |||| || | | || || |||| |||| || | || |||| | |||| | | | | |||||| || |||||||| |||||||||||||||||||| ||||| || ||||| |||||||| ||||||
gtacatatttaacgtcatatatgtgacttgttttctttaagttgtttcctgtttggt-ctaacgtagatggcctcacattaattgtcacagGCACTCAACTGACCGAGAGGTTGCCCTTATGATGCTTATGGCGTATCTTTCTTATATGCTTGCTGAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 4
-------gttag-ttaagcccaaacaaaccctcattagttaacggttttatgctcagtgttaacttggatgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
|| | || ||| || | | | || || || || || | || | | |||| | | ||||| || ||||| || || |||||||| |||||||| |||||||| |||||||||||||| ||||||
gtagataattggctttagctcatatgtgactttatct-ctattagtcttctgttatgt---agtctaa---ttgggtatctttcttagGCACTCGACTGATCGAGAAGTTGCCCTCATGATGCTTATGGCTTATCTTTCATATATGCTTGCTGAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 7
------------------gttagttaagcccaaacaaaccctcattagt-taacggttttatgctcagtgttaacttggatg-ttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
| | || | | | | | | || ||| | || || | |||| | || |||| | |||||||| |||||||| || |||||||||||||||||||| ||||| |||||||| || || || |||||
tttatgataaaacctcagatcatgtaggaatacatataataatacgagaataatcatactaaagacaaaatacacttacagaatttctgacaaaatccagGCACTCTACTGATCGGGAGGTTGCCCTTATGATGCTTATGGCATACCTTTCCTACATACTTGCTGAA
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 8
----------------------gttagttaagcccaaacaaaccctcattagttaacggttttatgctcagtgttaacttggatgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
|||| || | || ||| | | | ||||| | | | | | ||| | || | ||||||||||| ||||| || |||||||| | ||||| ||||||||||||||||| ||||||||||||||
attcttttatatcacttgtataagtagtaaatgtctaagaaaagacaa--gggctatagttttgaggagaattctcatactttctttgttaacaaactccagGCATTCGACTGATCGGGAGGTTGCAATCATGATACTCATGGCTTACCTTTCGTATATGCTGGCTGAA
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 7
---------gtta-gttaagcccaaacaaaccctcattagttaacggttttatgctcagtgtt----aacttggatgt------tggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
| | | ||| | | | | | | | ||| || | ||| | ||||| | | ||| | ||| |||||| |||||||| ||||| ||||| |||||||| ||||||||||||||||||| || |||||||
ggtcatattttcatatcaaggcaataaattgatggggtcatagaaggtgttttattcatcttcgcagaactttagtaactaaagttgtgcttaatttcagGCACTCTACTGATCGTGAAGTTGCACTTATGATTGTCATGGCTTACCTTTCATACATTATGGCTGAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|27549114|gb|CA767092.2|CA767092EST: GCTGGATTGCTCAGTGCATACATAATCAAGAAGCTATACATTGGAAG GCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTC
genomic: GCTGGATTGCTCAGTGCATACATAATCAAGAAGCTATACATTGGAAGgttagttaag ... ctgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagttaacggttttatgctcagtgttaacttggatgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
ttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttaagcccaaacaaaccctcattagttaacggttttatgctcagtgttaacttggatgttggtgactgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG