Sequence
atgc intronic sequence ATGC exonic sequence...gattatatgttatttattattaatttaatgtatttgatttttaacttgctatgccttatcattgcttttattaaccgatttgtgtccctaatcaatgcagTTTAAATTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
Basic information
species | Glycine max |
transcript | GLYMA19G41840.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 4
gattatatgttatttattattaatttaatgtatttgatttttaacttgctatgccttatcattgcttttattaaccgatttgtgtccctaatcaatgcagTTTAAATTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
| || | || || || | | ||| | || ||| || || | | | ||| || | | || ||||| ||| ||| ||||| || |||||||| || |||||||| || |||||| | |||||||| ||||| || ||||||||||| ||||| |||||| | || || ||||| |||
gtttgaaagtaatctaatgctg--ttactttaacggatattctgtttccattccaatatttttagtgt----gactgatttcccccccaaat--gtgcagCTTGAATTGGCAGCATCAGCTTTGTAAGAACCCTCGTCCAAATCCAGATATCAAAACTTTATTCACCGACCATACATGTTCTCCACCCAATGGAGCTCGT
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 3
--gattatatgttatttattattaatttaatgtatttgatttttaacttgctatgccttatcattgcttttattaaccgatttgtgtccctaatcaatgcagTTTAAATTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
| | | | | | | | | | | || || | | | ||| ||| | || | | | |||| || ||||| || |||||||| || || | ||| || || ||| | |||||||| ||||| || ||||||||||||||||| |||||||| || ||||| |||
cagctagcaccccctctcgcacggccctgtt--actgcacattctgttttcgttccgttacaatttttattgtgattatgatgccctccccaaaatgtgcagCTTGAATTGGCAGCATCAACATTGTAAGAATCCTCGTCCAAATCCAGATATCAAAACTTTATTCACTGACCATACATGTACTTTACCCAATGGAGCTCCT
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 4
gattatatgttatttattattaatttaatg--tatttgatttttaacttgctatgccttatcattgcttttattaaccgatt---tgtgtccctaatcaat-gcagTTTAAATTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
| |||| || || | | ||| ||| | | | | | | | || || |||| |||| | || | |||| | |||||||| |||||| | ||||| || ||||||||||| || ||||| || ||| ||||||| |||||||| || |||| ||| |||||||||||
----gtgtgtttcttttttctttcctcatgaccattctgtatgttgcagatgaggtttggatgacttcgttgttggatgattcattgtgcatatgttctcttgcagCCTCAATTGGCAGCACCAGTTGTGCAAGAATCCTAGGCCAAACCCAGATATTAAAACTCTATTCACAGACCACACTTGCACACTTCCGAATGGTCCTCTC
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
gattatatgttatttattattaatttaatgtatttg-atttttaacttgctatgccttatcattgcttttattaaccgatttgtgtccctaatcaatgcagTTTAAATTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
| | || | | | | || | | || | | || |||| | | | | | || || |||| | | |||||||||||||||||| |||||||||||||| ||||| |||||||||| || || ||||| |||||||| ||||| |||||| | ||| | ||||| ||||
-actttacatatactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------gattatatgttatttattat-taatttaatgtatttgatttttaacttgctat--gccttatcattgcttttattaaccgatttgtgtcc-ctaatcaat--gcagTTTAAATTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
|| || || | | | | | || | ||| ||| || || | |||| | | | | ||||| | | ||| || ||||| | |||||||| || ||||||||||||||||| ||||| ||||| || || ||||| | |||| ||| |||||||| ||||||||||| ||| |
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgctatgccttatcattgcttttattaaccgatttgtgtccctaatcaatgcagTTTAAATTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
attgcttttattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattatatgttatttattattaatttaatgtatttgatttttaacttgctatgccttatcattgcttttattaaccgatttgtgtccctaatcaatgcagTTTAAATTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
- - - - - - - - - - - - - - - - - - - - - - - - ctatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtccct