Sequence
atgc intronic sequence ATGC exonic sequence...gcatttttccatccacagcgtttgtcttccactttttagtttttactatctatctatttgctaatgagtgatttttcaatttgatgctttttgtgtgtagACTGAGTGGACGAGAGAAGAGGATGAGAAGCTACTTCATCTTGCTAAGCTTATGCCCACTCAATGGAGGACAATTGCTCCAATTGTTGGCCGTACCCCTT
Basic information
species | Glycine max |
transcript | GLYMA20G36600.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36600.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g28090.1 (Oryza sativa), 3'ss of exon 1
gcatttttccatccacagcgtttgtcttccactttttagtttttactatctatctatttgctaatgagtgatttttcaatttgatgctttttgtgtg----tagACTGAGTGGACGAGAGAAGAGGATGAGAAGCTACTTCATCTTGCTAAGCTTATGCCCACTCAATGGAGGACAATTGCTCCAATTGTTGGCCGTACCCCTT
| | | | || | | | | | || || || | |||| |||| || || | ||||| | | |||||| || ||||||| ||||| || ||||||||||||||| |||| ||||||||||| || ||||| || || |||||||||||||| || |||||||| || || || |
ggttctatttgagcataaccaattgcacttgcagatttgtcac-accaactat-tattctctcatt--ttattttctgtgctaactcttttttgttgatggcagACTGAATGGACAAGGGAAGAGGATGAGAAGTTACTGCATCTTGCTAAACTCATGCCTACGCAGTGGAGGACAATTGCACCTATTGTTGGTCGAACACCAT
upper sequence: GLYMA20G36600.2 (Glycine max), 3'ss of exon 1
lower sequence: AC203535.4_FGT001 (Zea mays), 3'ss of exon 1
gcatttttccatccacagcgtttgtcttccactttttagtttttactatctatctatttgctaatgagtgatttttcaatttgatgctttttgtgtgt-------agACTGAGTGGACGAGAGAAGAGGATGAGAAGCTACTTCATCTTGCTAAGCTTATGCCCACTCAATGGAGGACAATTGCTCCAATTGTTGGCCGTACCCCTT
| || || || | || | | ||| | ||| | | | | ||| | || | | | ||| | || | | | | ||| |||| |||||||| || || ||||||||||| |||||||||||||||| || ||||| ||||| |||||||||||||| || ||||| || || || || |
----tgctctattatgggcttatggcataggtctttct-tgtttgtcaccaagatgattgtttattgtt--tctctcactgtgctaactcatctatgttaatttcagACCGAGTGGACAAGGGAGGAGGATGAGAAATTACTTCATCTTGCTAAACTCATGCCTACTCAGTGGAGGACAATTGCACCTATTGTAGGTCGAACACCAT
upper sequence: GLYMA20G36600.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
-----gcattt--ttccatccacagcgtttgtcttccactttttagtttttactatctatctatttgctaatgagtgatttttcaatttgatgctttttgtgtgtagACTGAGTGGACGAGAGAAGAGGATGAGAAGCTACTTCATCTTGCTAAGCTTATGCCCACTCAATGGAGGACAATTGCTCCAATTGTTGGCCGTACCCCTT
||| || || ||| | | | || | ||| | || | | | |||| || ||||| | || || | || || | || ||||||| ||||| |||||||| |||||||| |||||||||||||| ||||| ||||| || |||||||| ||||||||||| |||||||| ||||| ||||
ttggtgcaattgatttcatt-gtaaaatcttatttttgcatttggttcatt--tgtttttctacac-ctggggagtggtgatttaact---cctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
upper sequence: GLYMA20G36600.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S641_1V6.1 (Physcomitrella patens), 3'ss of exon 1
gcatttttccatccacagcgtttgtcttccactttttagttt--ttactatctatctatttgctaatgagtgatttttcaatttgatgctttttgtgtgtagACTGAGTGGACGAGAGAAGAGGATGAGAAGCTACTTCATCTTGCTAAGCTTATGCCCACTCAATGGAGGACAATTGCTCCAATTGTTGGCCGTACCCCTT
||| | | || | | | | || |||| | || ||| | || | ||| || || ||| || ||| | |||| |||| || ||||| ||||||||||| ||||| || ||||||||||| || |||||||||||||| ||| | || ||| |||| || ||||| ||||| ||
taattaatgcttctcgggttagtattgcacgctagttagggtgattcttatttttcaggccg--gatgtgtctgttgaaaatctggaccttggtttgtgcagACGGAATGGACTAGAGAAGAGGACGAGAAACTCCTTCATCTTGCAAAACTTATGCCCACTCAGTGGCGAACTATTTCTCCCATAGTTGGTCGTACTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatctatctatttgctaatgagtgatttttcaatttgatgctttttgtgtgtagACTGAGTGGACGAGAGAAGAGGATGAGAAGCTACTTCATCTTGCTAAGCTTATGCCCACTCAATGGAGGACAATTGCTCCAATTGTTGGCCGTACCCCTT
tgcttttt CT-rich tract
atttttcaatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatttttccatccacagcgtttgtcttccactttttagtttttactatctatctatttgctaatgagtgatttttcaatttgatgctttttgtgtgtagACTGAGTGGACGAGAGAAGAGGATGAGAAGCTACTTCATCTTGCTAAGCTTATGCCCACTCAATGGAGGACAATTGCTCCAATTGTTGGCCGTACCCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - -tccatcc
- - - - - - - - -gcgtttg
- - - - - - - - - - - - -cttccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct