Sequence
atgc intronic sequence ATGC exonic sequence...tgcctggaccaacacatttcattcaactaaatactccaaattctgatggccgttttgattttgatgcctgtttgcatattctgtaaattgtaatatacagGAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGGCTATGGGCAAAGCGGCAAAACCATACCTATCGTCCTAATAGACCATTGA
Basic information
species | Glycine max |
transcript | GLYMA20G11330.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 11
------------------tgcctggaccaacacatttcatt--caactaaatactcca--aattctgatggccgttttgattttgatgcctgtttg---catattctgtaaattgtaatatacagGAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGGCTATGGGCAAAGCGGCAAAACCATACCTATCGTCCTAATAGACCATTGA
| | ||| | |||| | | || | | || | | | | ||| | | | | || ||| | || |||||||| | | |||| || |||||||| ||||||||||| ||||| ||||||||||||| ||| | ||||| ||| |||| ||||| || || | |||||| | |||||||
gtaaggtgtgcaaacaagttcttggttcgtagcattggaatgctaaatttctgctatacgagtacacatgcttctgtaaaatcaactggtaatttaacttctgttgaataaattgt--ttaatagGAGGAAGTTGCAAAGGAGTATGGCATCCCTGTACAATTTCAGCGCTTCTGGTTGTGGGCTAAGAGGCAGAACCACACATACAGGCCTAATCGTCCATTGA
upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 15
--tgcctggaccaacacatttcattcaactaaatactcc--aaattctgatggccgttttgattttgatgcctgtttgcatattctgtaaattgtaatatacagGAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGGCTATGGGCAAAGCGGCAAAACCATACCTATCGTCCTAATAGACCATTGA
| || | | ||| | | || | || |||||| | | ||| | | | | |||| || || |||| | | || ||||| ||||| || ||||||| ||| ||||| ||||||||||||| | |||||| ||||||||||| |||||||| || |||||||||||| | |||||||
catatttgctctatattattggctcttaatatgtggtcataaaattcatgtcacagttcttttatcagtttatgttggctaat--cataaa--gctacatgcagGAGGAGGTAGCTAAAGAGTTTGGTATACCAATTCAATTTCAGCGTTTTTGGCTGTGGGCAAAGCGCCAAAACCACACATATCGTCCTAATCGGCCATTGA
upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 15
---------------tgcctggaccaac--ac-atttcattcaactaaa--tactccaaattctgatggccgtttt----gattttgatgcct---gtttgcatattctgtaaattgtaatatacagGAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGGCTATGGGCAAAGCGGCAAAACCATACCTATCGTCCTAATAGACCATTGA
| || | | || || | || |||| | | | | || || |||||| | | | || ||| | ||| | | | ||||| || | || || ||| |||| | |||||| | | ||| || | |||||| ||||| ||||| |||||||| || |||||||||||||||||| | |
gcatgtccgcattattaccctaattagtcaacgatgccgtttaactgtgcttggtttcgactgaattgcttgtcactagagattttaacctcacaagcctgaataat-tgtgcgctcacttctgcagGAGGAAATAGCGAAGGAGCTTGGCGTCCCTGTTGAGTGTCAACGGTTTTGGCTTTGGGCGAAGCGCCAAAACCACACATATCGTCCTAATAGACCACTTA
upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 15
---tgcctggaccaacacattt-cattcaacta--aatactccaaattctgatggcc-----gttttgattttgatgcctgtttgcatattctgtaaattgtaatatacagGAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGGCTATGGGCAAAGCGGCAAAACCATACCTATCGTCCTAATAGACCATTGA
|| || | | | ||| ||| | || | ||| | | | | || || || | || | ||| | || | | ||| | |||||||| | ||||| || |||| | |||||| | | || | | ||||| ||||||||||| |||||||| || ||||||||||| |||||| | |
gtatgtcttctcagaaagttttacatccgtttataagcacttttactgataggaaacataatgtagtgtcttcgttgaatcattgagcaatcgtgcacctacaat-tgcagGAAGAAATCGCAAAGCAGCTTGGCGTCCCTGTTGAGTGCCAAAGGTTCTGGCTCTGGGCAAAGCGCCAAAACCACACATATCGTCCTAACAGACCACTAA
upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 13
tgcctggaccaacacatttcattcaactaaatactccaaattctgatggccgttttgattttgatgc-ctgtt-tgcatattctgtaaattgtaatatacagGAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGGCTATGGGCAAAGCGGCAAAACCATACCTATCGTCCTAATAGACCATTGA
|| | | | || ||| | | | ||| | | | || | | |||| || ||| | || |||| | | || || | | || | | |||||||||||| ||||| ||||||||||| || ||||| | ||||||||||
---------------------------------------------------gtctgtagcccaacgctctgctgtccgaattttttgactttgagcttttagGAGGAAGTTTCCAAGGAGTTCAACGTTCCCGTAAATTGCCAAAGGTTTTGGCTATGGGCTAAGCGTCAAAACCATACTTACCGTCCGAGCAGACCATTGA
upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 13
tgcctggaccaacacatttcattcaactaaatactccaaattctgatggccgttttgattttgatgc-ctgtt-tgcatattctgtaaattgtaatatacagGAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGGCTATGGGCAAAGCGGCAAAACCATACCTATCGTCCTAATAGACCATTGA
|| | | | || ||| | | | | | | | | || | |||| || ||| | || |||| | | || || | | || | | |||||||||||| ||||| ||||||||||| || ||||| | ||||||||||
---------------------------------------------------gtctgtagcccaacgctctgctgtccgaagtttttgactttgcgcttttagGAGGAAGTTTCCAAGGAGTTCAACGTTCCCGTAAATTGCCAAAGGTTTTGGCTATGGGCTAAGCGTCAAAACCATACTTACCGTCCGAGCAGACCATTGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|12774018|gb|BG238945.1|BG238945EST: AAGTGAGAAGTTTCAGAGTCCAAAAGCAGACATCTTTTAACCTTTTCAAG GAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGG
genomic: AAGTGAGAAGTTTCAGAGTCCAAAAGCAGACATCTTTTAACCTTTTCAAGgtatcttctt ... taatatacagGAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggccgttttgattttgatgcctgtttgcatattctgtaaattgtaatatacagGAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGGCTATGGGCAAAGCGGCAAAACCATACCTATCGTCCTAATAGACCATTGA
atattctgtaaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcctggaccaacacatttcattcaactaaatactccaaattctgatggccgttttgattttgatgcctgtttgcatattctgtaaattgtaatatacagGAAGAGGTTGCAAAAGAGTATGGCATACCTGTTCAATTTCAGCGCTATTGGCTATGGGCAAAGCGGCAAAACCATACCTATCGTCCTAATAGACCATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
tgcctgg
- - - - - aacacat
- - - - - - - - - -cattcaa
- - - - - - - - - - - - - - - - -ctccaaa
- - - - - - - - - - - - - - - - - - - - -tctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatat