Sequence
atgc intronic sequence ATGC exonic sequencegtcaaggcattttcttctaatttagtctcaaattactctcctttctctatgtagatgaaactaaaatttattttgcttggtgacattattgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
Basic information
species | Glycine max |
transcript | GLYMA02G04360.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
gtcaaggcattttcttctaatttagtctcaaattactctcctttctctatgtagatgaaactaaaattta--ttttgcttggtgacattattgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
| || | ||| ||| | | | | ||| | || | |||| || | | || || || ||| |||| ||||| |||||||| | || ||||| |||||||| |||||||| || |||| || ||||| |||||||| ||||||||||| || |||||||| |
-------------gtgcttgctcagttcttaatgattttt-tacctccagagagttttaactttcatctgactattatatgcctttttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
gtcaaggcattttcttctaatttagtctcaaattactctcctttctctatgtagatgaaactaaaattt-attttgcttggtgacattattg--cagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
| | | ||| ||| || | | |||| | | | || || |||| | | |||| | || || ||| ||||| || ||||| || ||||| || || || |||||||| || ||||||||||| | ||| ||||| || ||||| ||||| |||||||| |||||||| |
-----------gttattttattcagttcttgatgtgtatactttgacgttcaaaatttttctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 6
gtcaaggcattttcttctaatttagtctc----aaattactctcctttct--------ctatgtagatgaaactaa----aat--------ttattttgcttggtgacat-----tattgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
|| | | || || ||| | | | |||||| | || | || || || | |||| ||| || |||| ||||| | | | ||||||| |||||||| ||||| ||||||||||||||||| || || || ||||| || | ||| ||| | |||||||| || ||||||||||||||||||||||
gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 3'ss of exon 7
-gtcaag-gcattttcttctaatttagtctcaaattactctcct-----ttctctatgtagatgaaacta-----aaatttattttgcttggtgacattattgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
||||| || | || ||| || || || | | | || | |||| | ||| | | | || ||| | || | || ||||||| ||||||||| | ||| |||||||| |||||||| || || || || || ||||||| ||||||||||| || || ||||| ||| |||||||||
agtcaactacacaatattttaa---agactagaacagttgacgtgaagattttttatgca-atggatttgttgaggagttgattatcactgaaaagatg--tgcagGGATGTGATTGTCTGGGCCTGATCAAGTATTTTGATGCCCATTTTACCAATTTCCATGGAGGAGTTGAAACAATCGAAAACTGTGTCTGCATGCATGAAG
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S9_129V6.1 (Physcomitrella patens), 3'ss of exon 7
----gtcaaggcattttcttctaatttagtctcaaattactctcctttctctatgtagatgaaactaaaat--ttattttgcttggtgacattat-tgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
| | | | || || || | || | || | | | | | ||| | | | | || | | | | || |||||||||| |||||| | |||| || |||||||||||||| || || || ||||| ||||||| |||||||| ||||| || ||| ||||| |||| ||||
atcagctgctcaactcacgggcaacttgaacttca-ctatgcgagttgagttctttcaaaggaacagacttgctgagttgtcattgcgtagagatgtgcagGGTTGCGATTGTCTTGGCTTAATTAAGTACTTTGATGCACATTTTACCAACTTCCATGGAGGAGTTGAAACGATAGAAAACTGTATTTGCATGCACGAAG
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S363_39V6.1 (Physcomitrella patens), 3'ss of exon 5
gtcaaggcattttcttctaat--ttagtctcaaattactctcctttctctatgtagatgaaactaaaat-ttattttgcttggtg----acattattgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
| | ||| | | ||| | || ||||| | | | |||||| || || || |||| || | | ||||||| ||||||||| | || || || ||||||||||| || || ||||||||| ||||||| |||||||| || || || ||||| ||| |||||||||
-ttagagcagaacactgaagcccttacctttaagttactagaacacgtgagttgaaatgaaatgaacatgttgatttgattatcattcaaaaggtgtgcagGGGTGTGATTGTCTTGGTCTGATTAAATACTTTGATGCCCATTTTACAAACTTTCATGGAGGAGTTGAAACGATCGAAAACTGTGTCTGCATGCATGAAG
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S36_16V6.1 (Physcomitrella patens), 3'ss of exon 6
gtcaaggcattttcttctaatttagt-ctcaaattactctcctttctct-atgtag--atgaaactaaaatt--tattttgcttggt--gacattat------tgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
|| || | ||| || || | | || || | | | | ||| | | | || | || | | | ||| || || | ||||||||||||||||| | ||| | || |||||||| || ||||||||||| || ||| |||||||| || ||||||||||||||||| || ||||||| |
gtgaatg-attctcacaacgttcacttcttgggttcatgtgttctatcttacgcaatagtgcgatcaagtctgttgtattgacaaaacaaacgttgtgaactctgcagGGTTGTGATTGTCTTGGCCACATAAAGTACTTCGACGCTCACTTCACGAATTTTCTGGGAGGTGTGGAGACAATAGAGAATTGTGTGTGTATGCATGAGG
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S26_107V6.1 (Physcomitrella patens), 3'ss of exon 6
gtcaaggcattttcttctaatttagtctcaaatt---actctcctttctctatgtagatgaaactaa--aatttattttgcttggtgac---attattgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
|| |||| || || || || |||| | | | ||| ||| | | ||||||| || | | ||||||||||||||||| | ||| | || |||||||| || |||||||||||||| ||| |||||||| || ||||||||||||||||| || |||| || |
-gtgagtggttttgacgtagttgaggctttaatttacagggtttaatgactactcttgcgaacattactaatttatgacgcgctacctctgagcttctgcagGGTTGTGATTGTCTCGGCCACATTAAGTACTTCGACGCTCACTTCACAAATTTTCTGGGAGGTGTGGAGACAATAGAGAATTGTGTATGTATGCACGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttctctatgtagatgaaactaaaatttattttgcttggtgacattattgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
aactaaa putative branch site (score: 2)
tatgtagatgaaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaaggcattttcttctaatttagtctcaaattactctcctttctctatgtagatgaaactaaaatttattttgcttggtgacattattgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG