Sequence
atgc intronic sequence ATGC exonic sequencegtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
Basic information
species | Glycine max |
transcript | GLYMA11G08180.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
-----gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
||| | | || | || || || | | | | |||| | | || | || | || | ||| || | | || | | ||| || | |||||| ||||| ||||||||||| || ||||| ||||||||||| ||||||||| ||| || || ||||||||||| ||||| || || ||
gtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttc---attactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
upper sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
|| | | | | | || | | | | | | || || | || | || || | | || |||| | | | ||| | | ||| ||||| || |||| || |||||||| ||||| |||||||| |||||||||||| | || || |||||||| || || || || || ||||||||||| ||
-----aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcag-tgtaattgaaattaagttgc-cgcactc------------acagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
upper sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
| || || | || | | ||| || | || | | | | | ||| | || || | || | | | | ||| |||| ||| || || |||||||| |||||||||||||| ||||||||||| |||||||| ||| ||||| ||||||||||| ||||| || || ||
--------------------gtatctacttggggccatctgaatctgtcgg-gaatctgataggggca---agtctgcagtttag--ctgaccattttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
upper sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
|| | | || || || | |||||| || | | || |||| ||| | || ||||| ||| || | |||||| ||||||||||| ||||| |||||||| ||||| |||||||||||||| | ||| || || || |||||||| ||||||||||||||
--------------------------------------gttagtagcaaagtgatttaaagtttttcttgacatatc--------acttctttgatctaaccattatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
upper sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
| | | ||| || | ||| | || | | | || || || | | | | | |||||| ||||| || ||||| ||||| || || || || ||||| |||||||| |||||||| ||||| | |||||| || || ||||| || ||||||||||||||
------------------------------------gtaaaagtttcacttgtca--agtcttgtccctgagagcagaa--tggtagataatggaggtgattttgtgaaaatg--gcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT
upper sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 5
gtgagcaaaaatatgtgtt---aatcgtt--attttgt--tccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttat---ttgttctctctctttgaaaacaaa-acagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
|| || ||| | | || ||| | | |||| ||| | ||| ||| || || || ||| | | || || | ||| || | || ||| ||||| |||| |||||||||||||||||| ||||| ||||||||||| || ||||| || | ||| || || || || || |||||||| ||||||||||||||
gtaagtgaaatttcgccttctcaatatatggactttgaaatccatattttcatgggtttctgttgttcaaacaattacaacatatgcttctagcttttgaattggaaaaactgaatatgaataaacacagGGAAGAAGTTTCAAGATATTGTTGGTAGTGCCTACTATGTTGCTCCTGAAGTATTGAGACGGAAATCGGGACCTGAATCAGATGTCTGGAGTATTGGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
aatctttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG