Sequence
atgc intronic sequence ATGC exonic sequence...atgtgctgaacttgaacatcttttttgtattttatatttaaaaaatctttagtttttctagttttgagtcttgactatctaactttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
Basic information
species | Glycine max |
transcript | GLYMA09G32420.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G32420.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
atgtgctgaacttgaacatcttttttgtattttatat-ttaaaaaatct--ttagtttttcta-gttttgagtcttgactatctaactttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
| | ||| | | | ||| |||| || | | |||| || | | ||| | | | || | | | | | ||||| | |||||| |||||| || || | || | || || ||||| || ||||| || || || || || || || ||||||||||||||||| ||||||||||| |
-cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgc---cagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: GLYMA09G32420.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g22670.1 (Oryza sativa), 3'ss of exon 4
atgtgctgaacttgaacatcttttttgtattttatatttaaaaa--atctttagtttttctagttttgagtcttgactatctaactttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
| | |||| || | | |||||| | || ||||| | | | || || | | | || | ||| || | | | |||| || ||||| | | | | ||| ||||| || || || ||||| || || || || || ||||||||||||||||||||||| ||||| |
-tcttttgaattttcaaactcattttgtttggtagatttatatacaacattctcttcatgtgatatttttatgcatttgattaatcttaactgcacac-cagGATGATGCTGGAGCACCAGCCTCACTTCCAAAGCATAATAAAGGTTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAATGCTTTCAAGCAA
upper sequence: GLYMA09G32420.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G104246_T01 (Zea mays), 3'ss of exon 3
-----atgtgctgaacttgaacatcttttttgtattttatatttaaaaaatctttagtttttctagttttgagtcttgactatctaactttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
| | ||||| || | || || ||| |||| || | | || | || | | | || | | | | | | ||||| | ||||||| | || | || | || |||| || ||||| || ||||| ||||| || || || || |||||||||||||||||||| ||||||||||| |
ctatcaaatactgaaatt--atgtcattattgcatttaatttggaccaagttattgtgctgccatgacatgtggcattaattctagtccatgaaattgc---tagGAGGTGTCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGCCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: GLYMA09G32420.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 3
---atgtgctgaacttgaacatcttttttgtattttatatttaaaaaatctttagtttttctagttttgagtcttgactatctaactttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
| | | | || | ||| || ||| |||| || | | | || | || | | | | | | |||| |||| |||||| | || | || | || |||| || ||||| || ||||| ||||| || || || || || ||||||||||||||||| ||||||||||| |
atcaattacaggcatt--atatcattattgcatttcatttcggccatgttattgtgctgccttgacacgtcacattaat-tctagtccatgaaattttgccagGAGGTGCCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: GLYMA09G32420.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G388148_T01 (Zea mays), 3'ss of exon 3
atgtgctgaacttgaacatcttttttgtattttatatttaaaaaatctttagtttttct-----agttttgagtcttgactatctaactttgaaaataaatgt-agGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
|| || | | ||| | ||||| | || | | || |||||| | | || | || ||| |||| ||| | | |||| | |||| | ||| | ||| ||| || | || || |||||||| || || || || ||||| ||||||||||||||||||| |||||| |
-----cttaatccatatttgtttgtgctatttcccaaccaataca-ctctagtttctttgcttgagctgcatgtgaccactgcactacttgactaatgtctattagGATAATTCTGGAGCAGTCCCTCTCGTAGCAAAGCACCATAAAGGTTGTCATTGCAAGAAGTCAGGATGCCTAAAGAAGTACTGTGAATGCTACCAAGCAA
upper sequence: GLYMA09G32420.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
--atgtgctgaacttgaacatcttttttgtattttatatttaaaaa-atctttagtttttctagttt--tgagtcttg--acta-tctaactttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
|||| | || | || || | |||| | || | | ||| | | || | | | |||| | |||||| || | || ||||||| ||||| || | | | || ||||| ||||| || |||||||| || ||||| ||||||||||||||||| || |||||||||||||| |
tcatgtatt----ttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaacttt----attattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
upper sequence: GLYMA09G32420.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 5
atgtgctgaacttgaacatcttttttgtattttatatttaaaaaatctttagtttttctagttttgagtcttgactatctaac--tttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
|| | || | || |||| ||| || | || ||| || || | | | | | || | | | | || ||||||| | ||| || | | || || || ||||| || || || |||||||| || ||||||||||||||||| || ||||||||||||||||
-cgtattccttctgttgtaccaaattatattccatagtttcattatttttc-ttaacctgggcgagtggttgacgaaactgatggcatcttggttattgcagGAGGATGTTGGAGAGCATCCTCTGGCGGGCAAGCACAACAAAGGATGCCACTGTAAAAAGTCGGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttagtttttctagttttgagtcttgactatctaactttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
atctaac putative branch site (score: 2)
tatctaactttgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtgctgaacttgaacatcttttttgtattttatatttaaaaaatctttagtttttctagttttgagtcttgactatctaactttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- -tgctgaa
- - - - - cttgaac
- - - - - - - - - - - - - - - - - - - taaaaaa