Sequence
atgc intronic sequence ATGC exonic sequence...tgtcatgcgctttttccatccgactcattgattaagctgcttaattccaattatctgcctctagttcctggtttgcaatcattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGTGGTCTCTACAAAAAGCCAATGATAC
Basic information
species | Glycine max |
transcript | GLYMA10G33830.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g41370.1 (Oryza sativa), 3'ss of exon 1
--tgtcatgcgctttttccatccgactcattgattaagctgcttaattccaattatctgcctctagttcctggtttgcaatcattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGTGGTCTCTACAAAAAGCCAATGATAC
||| |||| | | | ||||| | || || | | | || || || ||| |||||||||| ||||||||||||||||| | |||||||| |||| | | || ||||| | ||||| || |||||||| ||||| || ||||| || ||| | |
atgagtgcatgctgtttctggggagatttatataagaactgct--agtcatatctagagaatacaattgacaacaatgtatggtttgctttaatttatgcagGTGGTGCAGTTGTTTTCATGTGTGGACAAGATAAGCTTTCTGGACTGGGCACCGGATTCAGAGTATATTCTATGTGGACTTTACAAGCGACCCATGGTGC
upper sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G07590.1 (Arabidopsis thaliana), 3'ss of exon 1
---tgtcatgcgctttttccatccgactcattgattaa-gctgcttaattccaattatctgcctctagttcctggtttgcaatcattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGTGGTCTCTACAAAAAGCCAATGATAC
| | | || | || |||| || | | | || | || | | |||| | || | | |||| || | || |||||||||||||| |||||||| |||||||| || || ||||| || |||||||| |||||||| || || |||||||||||||| || ||||| || ||||| |
tgctaaattttggaacttttaaccttagagatgataaatgtcgttgaagttt--ttttttctttctatgtactaatcttcaat-gttatggatg-tgaatgcagGTTGTGCAATTGTTTTCTTGCTTAGATAAAATAAGCTACATAGAATGGGCTCTTGATTCAGAGTACATTCTTTGTGGTCTTTATAAAAAACCGATGATTC
upper sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 2
---tgtcatgcgctttttccatccgactcattgattaagctgcttaattccaattatctgcctctagttcctggtttgcaatcattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGTGGTCTCTACAAAAAGCCAATGATAC
|| | | | | ||| | | || |||| || || | || || || | || || | | || || || || |||||||||||||| || || ||||| || ||||| ||||| ||||| ||||| |||||||| ||||| || |||||||||||||| || | ||||||||||
ggatggtaaac-catgttcttttttgttttttttttaaagatttttttttttttaatttgttggtaaataatgaaacttaa--aattttattttctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCTCTTGATTCAGAATACATACTTTGTGGTCTCTATAAGAGACCAATGATAC
upper sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S52_72V6.1 (Physcomitrella patens), 3'ss of exon 1
tgtcatgcgctttttccatccgactcattgattaagctgcttaattccaattatctgcctctagttcctg----gtttgcaatcattctttttggct---tatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGTGGTCTCTACAAAAAGCCAATGATAC
|||| || | | ||| | || || | | | || | | | | ||| | || |||| ||| | || | |||||||||||||||||| || ||||| ||||||||||||||| | |||||||||| ||||| || ||| |||| |||||||||| ||| | || | |
--tcata---ttccttgaatcga--aaatgggtatgaacttcagcatcagtgcttagatttggtttcttacaacaatttggatcacattttgggtctgggtttgcagGTTGTGCAGTTGTACTCTTGCTTGGACAAGATTAGCTATGTAGAATGGGCCCCAGATTCGGAGTATCTTCTATGTGGTCTCTTCAAGCGAGCTATTGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaattatctgcctctagttcctggtttgcaatcattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGTGGTCTCTACAAAAAGCCAATGATAC
attcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcatgcgctttttccatccgactcattgattaagctgcttaattccaattatctgcctctagttcctggtttgcaatcattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGTGGTCTCTACAAAAAGCCAATGATAC
- -catgcgc
- - - - - - - tccatcc
- - - - - - - - - - - - - - - - -aagctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtttg