Sequence
atgc intronic sequence ATGC exonic sequence...ctagccatgtaactgaagctgtgtgatataaattctaaacttatttccttttactttgcccccttttttgtgttactatatactaattgcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
Basic information
species | Glycine max |
transcript | GLYMA09G23250.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
---------------------------------------ctagccatgtaactgaagctgtgtgatataaattctaaacttatttccttttactttgccccctt------ttttgtgtt---actatatactaattgcttgcttg-cagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
| | | | |||| || | | | | |||| || | | || || || || | | ||| || | | | ||| || |||||| |||| || |||||||||||||||||||| || ||||||||||| || || | ||||||||| || || |||| || ||||| || ||| ||| |
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagct-tgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G159307_T01 (Zea mays), 3'ss of exon 10
ctagccatgtaactgaagctgtgtgat-----ataaattctaaacttatttcctt-ttactttgcccccttttttgtgttactatatactaattgcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
| || | | | || | || | | ||| | ||| || | || | || | ||| | | ||| || || | | | | | | || || |||||||| ||||| || |||||||| || || |||||||||||||| || ||| |||||| ||||||||||| |||||||
---gtaccgttattctggttgcataattcactgtgtaccctagatgaattaatttaccagttgacaatctgtaaattgtaattttattctt-ttctctattagGAAGGGACAGCAGATAATGAGTTTGAAAAGCGTATTAGACCAGAAGTGATACCTGCAAATGAGATTGGAGTTTCATTTGATGATATTGGTGCCTTGGATG---
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
ctagccatgtaactgaagctgtgtgatataaattctaaacttatttccttttactttgcccccttttttgtgttactatatactaattgcttgctt--gcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
||| | | | | | | | | || ||||| || | | | ||| | || |||||||||||| ||||| |||||||| ||||| || ||||||||||| || || |||| ||||||||| || ||||| | || || || || ||| || |
---------------------------gtaagtcgtcatcagttgactctgccccctgtgttcttttcctcaacgtta-acagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G058491_T01 (Zea mays), 3'ss of exon 10
-----------ctagccatgtaact---gaagctgtgt--gatataaattctaaacttatttcctt-ttactttgcccccttttttgtgttactatatactaattgcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
||| | | | || ||| | || | ||| | | | || | | || | || | ||| | | || | | | | | | | || || || |||||||| ||||| || |||||||| || || ||||| ||||| || || ||| |||||| ||||||||||| |||||||
gtaatgttattctaactgaatctttcagaaaattgttttctatgtgtgccctagaggaactaatttatcaattgtcagtctgtaacttgtacttttttatttttcttccattagGAAGTAACACCCGATAATGAGTTTGAAAAGCGTATTAGACCAGAAGTGATACCTGCTAATGAAATTGGAGTTTCATTTGATGATATTGGTGCCTTGGATG---
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv16s0050g01830.t01 (Vitis vinifera), 3'ss of exon 10
ctagccatgtaactgaagctgtgtgatataaattctaaacttatttcc--------ttttactttgcccccttttttgtgttactatatact---aattgcttgcttgcagGAAGTTCC---TGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
| || | | | || || | ||| || ||||||| | ||| | || | || || ||||| || | ||| ||||| | |||| || ||||||| ||| ||||| |||||||||||||| |||||| ||||||| || |||||| || |||||||| |||||||
-----------aaggaggttcccttgcatttgttttcccctttttgttgaagaaaattttactaagaaaattttccgatattcccttactcttttaattgtttcgctacagTTGGTTCCACCTTACAATGAATTTGAGAGGCGTATAAGGCCAGAGGTTATCCCAGCAAATCAGATAGGAGTGGCATTTGAGGACATTGGTGCCTTGGATG---
upper sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 12
ctagccatgtaactgaagctgtgtgatataaattctaaacttatttccttttactttgcccccttttttgtgttactata----tactaattgcttgcttgcagGAAGTTCC---TGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
|| |||| | ||| | | ||| | | | | |||| | | ||||| | | | ||| | | |||||| || | | ||||||||||| |||||| || ||||||||||| ||||| |||||||||||||| || ||||||||||| || ||||||| ||||| ||||| ||| ||
--gatcacaatgctgat-ttttgtaaaagaaaatttta-ttgggaaaattttccatcattcccttactcttttaactgttgaactgttaattgtttccctccagGAAGTTCCACCTGACAATGAATTTGAGAAGCGTATAAGGCCAGAGGTTATCCCAGCGAATGAGATAGGAGTGACATTTGATGATATCGGTGCTTTGAGTG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttttactttgcccccttttttgtgttactatatactaattgcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
tactaat putative branch site (score: 1)
cttgctt putative PPT
ttactatatactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagccatgtaactgaagctgtgtgatataaattctaaacttatttccttttactttgcccccttttttgtgttactatatactaattgcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - ccatgta
- - - - - - - gaagctg