Sequence
atgc intronic sequence ATGC exonic sequence...aatggcttttatacttttacattcaagatgcagttaaataggtagaataacagatgacaagtgaataatttctaaaattgattgcctttttttgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGGAGGAGGTGGAAGACATTA
Basic information
species | Glycine max |
transcript | GLYMA06G02110.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g44015.1 (Oryza sativa), 3'ss of exon 7
aatggcttttatacttttacattcaagatgcagttaaataggtagaataacagatgacaagtgaataattt--ctaaaattgattgcctttttttgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGGAGGAGGTGGAAGACATTA
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gatt-ttcttgtatgagtaatataagtatgttgtctatttagtttg-tagtggtttccttttttttccttttccctaaacagtctttctcttgggttgccagATTTGAACCTGATATGCTTGCATTTTCGGGGTGCTATTATGGTGGTGGAGAAAAAGAAAGAAAAGAGCTTGGTGCAATACGGAAGAGATGGAAAACCTTG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 10
-aatggcttttatacttttacattcaagatgca-gttaaataggtagaataacagatgacaagtgaataatttctaaaattgattgcctttttttgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGGAGGAGGTGGAAGACATTA
| | | || | | ||||| | ||| | | | | | | || | | ||| | || | | || | | ||| ||||||||||| |||||||| |||||||| ||| |||||||||| || || |||||| | | ||||| || | || | | | | ||||| || ||
aagtagagactaaaata--acatttcatatgtacactcttcctcttgcactatgcatcattttgctctttttttcagcatgcaccgtctatcctgatggcagGTTTGAACCTGACATGCTTGCCTTTTCTGGGTGTTATTATGGTGGTGGAGAAAAGGAGAAAAGAGAACTAGGCTCCATTCGCAAGCGATGGAAAACTTTG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G168614_T01 (Zea mays), 3'ss of exon 6
aatggcttttatacttttacattcaagatgcagttaaataggtagaataacagatgacaagtgaataattt--ctaaaat-tgattgcctttttttgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGGAGGAGGTGGAAGACATTA
|| | ||| | |||| | | | || || | | || | | | || || | || | || ||| | || | ||||||||||||||| |||||||| |||||||| || |||||||||| || || |||||| || ||| | | |||||| | || | |||| || ||
-gtgaaatatatcttgttacttctttattactattccgtaca-acattagctcgttttgtttctatttcttgaccaagacatggttgt-tgttctgatggcagATTTGAACCTGACATGCTTGCCTTTTCTGGGTGCTATTATGGTGGTGGAGAAAAGGAGAGGAGAGAATTAGCTGCAATTCGCAGACGATGGAGAACCTTG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G131699_T01 (Zea mays), 3'ss of exon 7
aatggcttttatacttttacattcaagatgcagttaaataggtagaataaca--gatgacaagtgaataatttctaaaattgattgcctttttttgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGGAGGAGGTGGAAGACATTA
| | || ||| || | |||| || | ||| | | ||| | ||||| ||| | |||||| |||||| ||||||||||||||||| ||||| || || |||| ||||| || ||||| ||| || ||||| ||||| ||||||| ||||||||| ||
--ttacaaataccttttctcagcgcatatgcgtttcctttacggtaatgatattgattttttcttgtccctttcttaaacattattccttttgcaatgtcagATTCGAACCTGATATGCTTGCCTTTTCGGGGTGCTATTACGGTGGTGGAGAGAAAGAGAGGAGAGAACTTGGTGCTATAAGGAAGAGGTGGAAAGGCTTG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 6
aatggcttttatact--tttacattcaagatgcagttaaataggtagaataacagatgacaagtgaataatttctaaaattgattgcctttttt-tgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGGAGGAGGTGGAAGACATTA
|| | ||| || | ||| | | ||| ||| || | | | || | | || | | | | | || || || | ||| | ||||||||||||||||||||| || ||||| |||||||||| || || ||||| || ||||| | ||||| || ||||| ||||| ||||||
-atttttgatattctagtcaacaattatgatatt-ttacatttacctcttgaatctctataaat-actagtgtttgacgcaagtgatattgattgtgttgcagGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g00100.t01 (Vitis vinifera), 3'ss of exon 7
----------aatggcttttatacttttacattcaagatgcagttaaataggtagaataacagatgacaagtgaataatttctaaaattgattgcctttttttgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGGAGGAGGTGGAAGACATTA
|||||| | | ||| | |||||||| | | || || | | || ||| || | ||| | || ||| ||| ||| |||| |||||||| |||||||||||||| || ||||| | |||||||| || || ||||| ||| || |||||||||||| | | ||||||||| || |||
atgaacaagtcatggctatatgattttaatattcaagaaactgccaattatg------agaaggtgagaa--agtttctttatgccatcagatgc--tttgttgtcacagGTTTGAACCCGATATGCTTGCATTCTCAGGATGCTACTATGGTGGGGGAGAAAAGGAAAGGAAAGAGCTGGGTGCAATACGAAAGAGGTGGAAAACTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataacagatgacaagtgaataatttctaaaattgattgcctttttttgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGGAGGAGGTGGAAGACATTA
ttgcctttttttgct CT-rich tract
tgaataatttctaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatggcttttatacttttacattcaagatgcagttaaataggtagaataacagatgacaagtgaataatttctaaaattgattgcctttttttgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGGAGGAGGTGGAAGACATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - acattca
- - - - - - - - - - - - - gatgcag
- - - - - - - - - - - - - - - - - - - - - - gaataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgacaag