Sequence
atgc intronic sequence ATGC exonic sequence...cagtgtttgctataaattgttatcatttattctcttgtaatcggtgatatcctcttgttggttttttcactaccagctctgacttctaataaacatgcagATCAACGCCTCAATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGCTCCATAGATCTTATAGTGTTGAAGGAGACTTATGGAGTATTGGGGT
Basic information
species | Glycine max |
transcript | GLYMA06G13920.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G13920.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g36710.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------------cagtgtttgctataa-attgttatcatttattctcttgtaatcg----gtgatatcctcttgttggttt--tttcactaccagctctgacttctaa-----taaacatgcagATCAACGCCTCAATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGCTCCATAGATCTTATAGTGTTGAAGGAGACTTATGGAGTATTGGGGT
| |||| | | || || | || | | ||| || | |||| | || ||| | ||| | | ||| | | | | | ||||| || | | |||||||||||||| ||||| ||||||||||| || ||||| || ||||| || ||||| |||| |||| | ||||||||||| ||
gtatttccccccaaaagaattatgcccttccaaagaacttgtgtttcatcttatgttttttttttactctattatgaatttgtcctgacatggtgaaaatactgttttttgaaaccaaatagtgaaaatactcaagtgttttgatgacacacatatttatgattggtcaatgccttcttttacagATGAAAGATTAAATGATATTGTTGGTAGTGCATACTATGTTGCTCCAGAAGTCCTACATAGGTCATATAGCACGGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: GLYMA06G13920.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G115518_T01 (Zea mays), 3'ss of exon 5
cagtgtttgctataaattgttatcatttattctcttgtaatcggtgatatcctcttgttggttttttcact--accagctctgacttctaataaaca-tgcagATCAACGCCTCAATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGCTCCATAGATCTTATAGTGTTGAAGGAGACTTATGGAGTATTGGGGT
| | |||| || ||| || || | || | || || | | | | | || ||| | | || | | || || ||||||| || | ||||||||||||||||| |||||||| |||||||| || || || || || ||||| || ||| | |||| |||| | |||||||| || ||
tggaatacactatcaacatttacagttaatattttttt--tcagtt-cactcattaactaaatcttatacttaattttgtgtgttctgcactatgcaatgcagATGAAAGGCTCAATGATATTGTTGGAAGTGCTTATTATGTTGCTCCAGAGGTTCTACACAGATCATACAGTATGGAAGCAGACATTTGGAGTATAGGTGT
upper sequence: GLYMA06G13920.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G24430.1 (Arabidopsis thaliana), 3'ss of exon 5
cagtgtttgc-tataaattgttatcatttattctcttgtaatcggtgatatcctcttgttggttttttcactaccagctctgacttctaa------taaacatgcagATCAACGCCTCAATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGCTCCATAGATCTTATAGTGTTGAAGGAGACTTATGGAGTATTGGGGT
|| ||| || |||| | ||||| | || || | | |||| | || || ||| | || | | || | |||||||||| || ||||||||| |||| || ||||| |||||||||||||||||||| |||||||| ||||| || ||||| ||| | ||||| || || ||
--gtaaccatatatgttcccttggcattattagtcttgcca-----aatctcatttgtacaagttttccgctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
upper sequence: GLYMA06G13920.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
cagtgtttgcta--taaattgttatcatttattctcttgtaatcggtgatatcctcttgttggttttttcactaccagctctgacttctaataaacatgcagATCAACGCCTCAATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGCTCCATAGATCTTATAGTGTTGAAGGAGACTTATGGAGTATTGGGGT
|| | || || | | | | | ||||| | | | | | ||| | | | | | | ||| || | || ||||||||| ||||||||||||||||| ||||| |||||||||||||| ||||| ||||| ||||| || | | |||||| || | ||||| ||||| ||
-tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgt-aacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatcctcttgttggttttttcactaccagctctgacttctaataaacatgcagATCAACGCCTCAATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGCTCCATAGATCTTATAGTGTTGAAGGAGACTTATGGAGTATTGGGGT
ttctaat putative branch site (score: 2)
ttctaataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagtgtttgctataaattgttatcatttattctcttgtaatcggtgatatcctcttgttggttttttcactaccagctctgacttctaataaacatgcagATCAACGCCTCAATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGCTCCATAGATCTTATAGTGTTGAAGGAGACTTATGGAGTATTGGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgactt