Sequence
atgc intronic sequence ATGC exonic sequence...gattgttgttttgttccttgagcttattctgcttgtttttttttaatcagcagcttattctgtttgtgaaatggaaaactaataaatcatattattttagTATGTTATCTTTCGACGTGGCATTGGAATTGATCGAACAACTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
Basic information
species | Glycine max |
transcript | GLYMA19G27800.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g29550.1 (Oryza sativa), 3'ss of exon 5
--gattgttgtt--ttgttccttgagcttattctgcttgtttttttttaatca-gcagcttattctgtttgtgaaatggaaaactaataaatcatattattttagTATGTTATCTTTCGACGTGGCATTGGAATTGATCGAACAACTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
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tttattacacttgcctgtcccacaaggacagtaag-tcatttttttctgctaatgctggagaatattcttattttattttacactggc----cacatttttgcagTATATTATCTTTCGTCGGGGCATTGGAATTGACCGTACAACCGATTACTTTATCATGGAGAAACTGGATGTGATCATATCCCGAGCTTGGAGCTCATTGC
upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G011136_T03 (Zea mays), 3'ss of exon 5
-----------------------------------------------------gattgttgttttgttccttgagcttattctgcttgttttt-ttttaatcagcagcttattctg--tttgtgaaatggaaaactaataaatcatattattttagTATGTTATCTTTCGACGTGGCATTGGAATTGATCGAACAACTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
|| | || || | | | || |||||| | | || | || | || || | | | | | || || || || |||||| | |||||||| || ||||||||||||||||||||||||||||||||| | || |||||||| || | | || || |||| | |
gtattattcgttcatgcaacttttcttttcatcctgatgatacttatgtttatgagggatgattagaaatctacaatagcattggatgttttcatcatcctctgttttttctcatggtttcctaagacacattcttcattgtccacatc-ttgtagTATATCATCTTTCGTCGGGGCATTGGAATTGATCGAACAACTGACTACTTTTTCATTGAGAAAGTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGC
upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G527387_T01 (Zea mays), 3'ss of exon 5
-gattgttgttttgttccttgagcttattctgcttgtttttttttaatcagcagcttattctgtttgtgaaatggaaaacta-ataaatcatattattttagTATGTTATCTTTCGACGTGGCATTGGAATTGATCGAACAACTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
||||| |||||| | | || | | | || ||| || | | ||||| | || | | | | | | | | || || ||||| ||||||| || || |||||||| |||||||| |||||||||||||| | |||||||||||||| | | || || ||| | |
aatttgtttgcttgttc--taattttgtcttcacaagtattatttcctcggtattttattatagttttcagcagttatttcacgtcaccaacatctttacagTATATTATCTTCCGTCGGGGCATTGGGATTGATCGGACAACTGACTACTTCTTCATGGAGAAAGTGGATGTCATCATATCCCGAGCATGGAGGTCATTGC
upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
gattgttgttttgttccttgagcttattctgcttgtttttttttaatcagcagcttattctgtttgtgaaatggaaaactaata-------aatcatattattttagTATGTTATCTTTCGACGTGGCATTGGAATTGATCGAACAACTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
|| | ||| | | | | | | | | | || || ||| | | | ||||||||| | | || | ||| ||||||| ||||| |||| ||||||||||| ||||||||| |||| |||||| | |||||||||||||||||| | ||| ||| | ||| | || |
-----atgcaatcttcatacaatgcagttaaccttcctcctcctcctc--tctctctctctcccaaaaagaagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcagcagcttattctgtttgtgaaatggaaaactaataaatcatattattttagTATGTTATCTTTCGACGTGGCATTGGAATTGATCGAACAACTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
aactaat putative branch site (score: 2)
ttatttt putative PPT
aaatggaaaactaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattgttgttttgttccttgagcttattctgcttgtttttttttaatcagcagcttattctgtttgtgaaatggaaaactaataaatcatattattttagTATGTTATCTTTCGACGTGGCATTGGAATTGATCGAACAACTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - tgttttg
- - - - - - -ttccttg
- - - - - - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaac