Sequence
atgc intronic sequence ATGC exonic sequence...ttagcttaccttagtcatgtgttgtctggttgttggtataagaaaattgacgagtcatgcatgtgttgatgatgcatgcatgcgcaatattaatgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
Basic information
species | Glycine max |
transcript | GLYMA19G34880.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G34880.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g33760.1 (Oryza sativa), 3'ss of exon 1
ttagcttaccttagtcatgtgttgtctggttgttggtataagaaaattgacgagtc-atgcatgtgttgatgatgcatgcatgcgcaatattaa---tgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
||| | | || | | | ||| || | | ||| || | |||||| || | | | |||| | |||||||||||||||| | ||| | ||||||||||||||||| ||| | ||||| ||||||||||| |||| ||||| ||||| || || | | || ||
ttaatgaagggt-gtaacatagcactaaatggtt---attaattagctgatgattggatgcatatgagagcttaattagtttttattttgttaacttttttcagAGGTGGCTAAGCTCACTGCAGAGGAGTGGTACTTCTTCAGCTTCAGAGACCGGAAATATGCGACAGGGTCACGGACGAACCGTGCGACCAAGACAGGTTA
upper sequence: GLYMA19G34880.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g56600.1 (Oryza sativa), 3'ss of exon 1
-ttagc-ttaccttagtcatgtgttgtctggttgttggtataagaaaattgacgagtcatgcatgtgttgatgatgcatgcatgcgcaatattaatgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
||| ||| | | | | | |||| | | ||| | | || | || | || ||||| || | | | | |||| ||||| ||||||| |||| ||||||||||||||||| ||||| |||||||| || ||||||||| | || || ||||| || || | || || ||
gctagtattataccacatactgaatatattacggttgatctcagattagtctagattaat-cgagttgtgatg-tgaaaaattaattatggtgtgcatgcagATGTGGCGAAGCTGAGCACGAACGAGTGGTACTTCTTCAGCTTCCGCGACCGCAAGTACGCGACGGGGCTCCGCACGAACCGCGCCACCAAGTCCGGCTA
upper sequence: GLYMA19G34880.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g43560.1 (Oryza sativa), 3'ss of exon 1
ttagcttaccttagtcatgtgttgtctggttg-ttggtata-agaaaattgacgagtcatgcatgtgt-tgatgatgcatgcatgcgcaatatta-------atgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
| | ||| | | | | || | || | | | || ||| || | | | | | |||| | | | |||| | |||| ||||| ||||||| |||| ||||||||||||||||| ||| ||||||| || || |||||||||| || || ||||| || || | | || ||
----------tcatgtatgcaaagccagactaattcgcatgcactatctcaacttctcaagcccctctctaacaacgcattcgttcttgctattctttgcgcacatgcagACGTGGCGAAGCTGACGGCGAGCGAGTGGTACTTCTTCAGCTTCAGGGACCGAAAGTACGCGACGGGGTCGCGCACGAACCGCGCCACCAAGACAGGCTA
upper sequence: GLYMA19G34880.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G062009_T01 (Zea mays), 3'ss of exon 1
-------ttagcttaccttagtcatgtg--ttgtctggttg--ttggt--ataagaaaattgacg----agtcatgcatgtgttga--tgatgcatgcatgcgcaatatta---atgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
| ||| | || | ||| | || | | ||| | ||| || || | || || |||||| || | | | || | | | | |||||||||| ||||||| || | ||||||||||||||||| |||||||||||||| || || ||||||| || |||||||| || || | |||| ||
gtcagttcgtacgtacgtgtgtgaagtgaactagctagctagcttgatcgatatgatcatcgtcgtcgtcgtggtgcatgcgtctaattaactggtgggtcgtcggtgcggtgcgcgtgcagAGGTGGCGAAGCTGACGGCCACCGAGTGGTACTTCTTCAGCTTCCGGGACCGCAAGTACGCCACGGGGTCGCGCACCAACCGCGCCACCAGGACGGGCTA
upper sequence: GLYMA19G34880.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G062009_T02 (Zea mays), 3'ss of exon 1
ttagcttaccttagtcatgtg--ttgtctggttg--ttggt--ataagaaaattgacga----gtcatgcatgtgttga--tgatgcatg---catgcgcaatattaatgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
| ||| | || | ||| | || | | ||| | ||| || || | || || |||||| || | | | || | | | | | |||||||||| ||||||| || | ||||||||||||||||| |||||||||||||| || || ||||||| || |||||||| || || | |||| ||
-gtacgtacgtgtgtgaagtgaactagctagctagcttgatcgatatgatcatcgtcgtcgtcgtggtgcatgcgtctaattaactggtgggtcgtcggtgcggtgcgcgtgcagAGGTGGCGAAGCTGACGGCCACCGAGTGGTACTTCTTCAGCTTCCGGGACCGCAAGTACGCCACGGGGTCGCGCACCAACCGCGCCACCAGGACGGGCTA
upper sequence: GLYMA19G34880.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G081930_T01 (Zea mays), 3'ss of exon 1
ttagcttaccttagt-catgtgttgtctggttgttggtataagaaaattgacgagtcatgcatgtgttgatg-atgcatgcatgcgcaatattaatgca---cagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
| || || |||| || | | | | ||| | | || || | | || | ||| | | | | | || | ||| || |||| | ||| ||||||| |||| ||||||||||||||||| |||||||||||||| || || ||||||| || |||||||| || || | |||||||
---acacacgcatgtacatgcattatataaattcttatatcgtacgct--actagctagctagctgctaatggacacgtacgtacgtacgtcgaatacatgtcagACGCGGCCAAGCTGACGGCGAGCGAGTGGTACTTCTTCAGCTTCCGGGACCGCAAGTACGCCACGGGGTCGCGCACCAACCGCGCCACCAAGACGGGGTA
upper sequence: GLYMA19G34880.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G857701_T01 (Zea mays), 3'ss of exon 1
----ttagcttaccttagtcatgtgttgtctggttgttg-gtataagaaaattgacgagtcatgcatgtgttgatgatgcatgcatgcgcaatattaatgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
| | | | | | | | | || | | || |||| | | | | ||||| || ||| ||| | |||| ||||| ||||||| |||| ||||||||||||||||| ||||| |||||||| || || |||||| | || |||||||| || || | || || ||
gtgtgaaaatcaacacgaacgc-taaaatttcatcgtcgtacctgtgatgattgcttttctactaacgcgcgactgatgagtg-atg---aatccatggtcgcagACGTGGCGAAGCTGAGCACGAACGAGTGGTACTTCTTCAGCTTCCGCGACCGCAAGTACGCCACGGGGCTGCGCACCAACCGCGCCACCAAGTCCGGCTA
upper sequence: GLYMA19G34880.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G140901_T01 (Zea mays), 3'ss of exon 1
-ttagcttaccttagtcatgtgttgtc--tggttgttggtataagaaaattgacgagtcatgcatgtgttgatga-tgcatgcatgcgcaatattaatgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
|| | | || || | | | | | | || ||| || || | || | || |||||| | ||||||| ||| ||||| ||||| ||||| ||||||| | || || |||||||||||||| ||||| |||||||| || ||||||||| || ||||||| || || | ||||| ||
tccagttaatagtaaacaccgaataccgattgctctacacatctgaagcttactgactgataaac-tgatgatgaatccatgcatacgcg-tattaca--acagACGTGGCGAAGCTGAGCACCAACGACTGGTACTTCTTCAGCTTCCGCGACCGCAAGTACGCGACGGGGCAGCGCGCCAACCGCGCCACCAGGTCGGGCTA
upper sequence: GLYMA19G34880.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G043813_T01 (Zea mays), 3'ss of exon 1
ttagcttaccttagtcatgtgttgtctggttgt-tggtataagaaaattgacgagtcatgcatgtgttgatgatgcatgcatgcgcaatattaatgc--acagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
| | || | | || | |||| | | || ||||| | || | | | | || ||| | | || ||| |||| | ||| ||||||| |||| ||||||||||||||||| ||| |||||||||| || ||||| ||| || || ||||| || || | |||| ||
---gatcacttatctgcctaattaacacgttgaattaaacaaataaatttgctctatatacttattatatgtatatatggtgtctcgatcgatatgatatcagACGCGGCCAAGCTGACGGCGAGCGAGTGGTACTTCTTCAGCTTCAGGGACCGCAAGTACGCGACCGGGCCGCGCACGAACCGCGCCACCAAGACGGGCTAMapped 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|151394219|gb|EV264090.1|EV264090EST: TACCTTGGTCGAAATTGACCTCCACATATGCGAACCTTGGCAACTTCCAG AGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACC
genomic: TACCTTGGTCGAAATTGACCTCCACATATGCGAACCTTGGCAACTTCCAGgtaaatatat ... taatgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgacgagtcatgcatgtgttgatgatgcatgcatgcgcaatattaatgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
tattaat putative branch site (score: 2)
aatattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagcttaccttagtcatgtgttgtctggttgttggtataagaaaattgacgagtcatgcatgtgttgatgatgcatgcatgcgcaatattaatgcacagAGGTGGCTAAGCTGAATGCGAATGAGTGGTACTTCTTCAGTTTCCGGGACCGCAAATATGCGACGGGGTTTCGGACCAACCGGGCAACTACATCGGGGTA
- -gcttacc
- - - - - - agtcatg
- - - - - - - - - -tgttgtc
- - - - - - - - - - - - - - gttgttg
- - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgca