Sequence
atgc intronic sequence ATGC exonic sequencegtctgttgatttttgcaaatggtatccctaaattgtttgttattctggttttgcactataccacatgggtcctttatttatttctgattatggaatatttatttcccttttatctttctctagGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
Basic information
species | Glycine max |
transcript | GLYMA14G29810.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 9
gtctgttgatttttgcaaatggtatccctaaattgtttgttattctggttttgcactataccacatgggtcctttatttatttctgattatggaatatt-----------tatttcccttttatctttctctagGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
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--gttctgatttctg--agccctttctctaaac-atgtgttgctctgagcttaatctcacccagtttg--cccttatgatttctagatcgtagtgtgttgccttgttaaacattcatagtttccctctttacagGCGCCATGCATTGTTTTCATTGATGAAATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCG
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 9
gtctgttg-atttttgcaaatggtatc-cctaaattgtttgttattctggttttgcactataccacatgggtcctttatttatttctgattatggaatatttatttcccttttatctttctctagGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
||| || || | || || |||| | ||| | | ||| || | | | | | | | ||||| | | | || | | |||||| |||| |||| || || ||| |||| ||||||||||| |||||||| |||||||| || ||||| ||||| || ||||||||||||||||||||||| || |||||||
---agttatatattggaaactgatatcgtccaaagaatcttatatacttg------aagagaggagaatgccgctttagccagcttt--------aacaatcatttcctctttac--------agGCACCATGCATTGTTTTCATTGATGAAATAGATGCTGTGGGATCAACTAGGAAACAGTGGGAAGGGCACACAAAGAAGACATTGCATCAACTTCTTGTTG
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 9
gtctgttgatttttgcaaatggtatccctaaattgtt-tgttattctg-gttttgcactataccacatgggtcctttatttatttctgattatgg-aatatttatttcccttttatctttctctagGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
||| || || || || | |||| | ||| | | | | | | | | | | ||||| | || | | | ||| | | |||| || || ||| | || ||||||||||| |||||||| || ||||| |||||||| ||||| || |||||||||||||| |||||||| || |||||||
--------------------------gataagttattctgaaatgcaatattttatgttttactgacttaataccatgaaaactaaaggtcaaagtaatatattttaacaatctttctctttacagGCGCCATGCATTGTCTTCATTGATGAAATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGGCACACAAAGAAGACGTTGCATCAACTTCTTGTTG
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 9
gtctgttgatttttgcaaatggtatccctaaattgtttgttattctggttttgcactataccacatgggtcc--tttatttatttctgattatggaatatttatttccctt--ttatctttctcta--gGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
|||| || || | ||| | ||| || | |||| | | | || || ||| | || | ||| ||||| | | ||| | || ||| |||||||||||||| ||||| |||||||||||||||||||| ||||||||||||||||| || || |||||||||||||||||||| ||||||||||
---------------------gtatgactcaact---tgtca--ctgcttatcagctattttaaaagagtttggttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 9
gtctgttgatttttgcaaatggtatccctaaattgtttgttattctggttttgcactataccacatgggtcctttatttatttctgattatggaatatttatttcccttttatctttctctagGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
||| || | || | | || | ||| | | | || | ||| || || | ||| | || | | |||| || |||| | |||| ||||||||||| || ||||| ||||||||||| |||||||||||||| ||| |||| |||||||| ||||| ||||| || |||||||| || || |||||||
--------ctttatgtagat--ttttactta--tgtacatggtgttaattcgg----atatggaattggagatccattaaattttagct------cattttttgtactttcttatttca-tagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S9_238V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------gtctgttgatttttgcaaatggtatccctaaattgtttgttattctggttttgcac-tataccacatgggtcctttatttatttctgattatggaatatttatttcccttttatctttctctagGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
||| | | || | | | ||| || || | | |||| ||| ||| | | | | || || | || ||| ||| | | |||||||||| || | |||||||||||||||||||||||||| | | || |||||||| ||||| || || || || || ||||| | || || |
gtacatttcgtataaaccaatacccttgtataatattctcttttacactctcgtattcattcttcaaaagaatctgcatatatgatttgctggttttacagagaacttcagttctgtggttttgattgattgtttgtg--gcgacagGCTCCTTGCATCGTCTTTATTGATGAAATTGATGCTGTTGGGGGCAGCCGCAAGCAATGGGAAGGCCATACGAAAAAAACTCTGAATCAGTTGCTGGTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcctttatttatttctgattatggaatatttatttcccttttatctttctctagGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
ttctgat putative branch site (score: 3)
tatttatttccctttt putative PPT
ttatttatttctgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgttgatttttgcaaatggtatccctaaattgtttgttattctggttttgcactataccacatgggtcctttatttatttctgattatggaatatttatttcccttttatctttctctagGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
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