Sequence
atgc intronic sequence ATGC exonic sequence...atgatcaaatatttgagcctatcataacttgcatcttcaatttcatgtacatttcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA
Basic information
species | Glycine max |
transcript | GLYMA03G34340.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
atgatcaaatatttgagcctatcataacttgcatcttcaatttcatgtacatttcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA
|| || |||| |||| ||| | | || |||||| | | ||| ||| || | || |||||||||||||||||||||||||| || ||||| ||||| || || ||||| |||||||| |||||||| |||||||| ||| | || | || | ||||| |
--------gtaacgga-tttatctacactt----ctttagctccaatcccatttctt---gcgcagtgacaatcctt-aacac----ttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 5
atgatca--aatatttgagcctatcataactt--gcatcttcaatttcatgta----catttcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA
| | | | || | || || | | | |||| | ||| || | | | | ||| | | | | ||||||||| | ||||||||||| ||||||||||||||||| ||||| ||||| || || || ||||| |||||||||||||| ||||| || || | || | || | || || |
gtaactattgacatcagcaccaatttcacttgaggtttctttagtttaattttcccccttcctttttaatgtaatgatccttcttgaatat----ctgcaaattgcagTTTCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATCCACCGGAGGTTTGATTTGAAAGGATCATCTTTAGGCCGTTCTACTGATAAAA
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 5
atgatcaaatatttgagcctatcataacttgcat---cttcaatttcatgtacatttcctcaaataggaggctaatacttgaat----atgat-tttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA
| || | || ||| | |||| ||||| || || || | | | | || | ||||| | | ||||||| || ||||||||||||||||| ||||| ||||| || || || || || |||||||||||||| ||||| || || | || | || | ||||| |
--------------------gtaatgatttacatgagcatcaaattcatttaaggtttctttagtttagtttttaccctccctttttaatgatatctgcaaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
---atgatcaaatatttgagcctatcataacttgcatcttcaatttcatgtacatttcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA
| | | | | | || |||| | | | ||| | | | ||||| ||| | | || | || ||||||||||||||||| ||||||||||| |||||||||||||| ||| | |||||| |||| |||||||| |||||||| ||| | || | || ||||||||
attcttgttggcttatccaaaaaaacaaaact---actgttgagcatatgattgcatatatgtacaatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ34272 (Selaginella moellendorffii), 3'ss of exon 4
atgatcaaatatttgagcctatcataacttgcatcttcaatttcatgtacatt-tcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA
||| | ||| |||| |||| || | | | | || ||| || || ||| |||| ||||| ||||||||||| ||||||||||||||| | | || || |||||||| ||||| || || || || || || | || | || ||
---------------------------------------gtttgagttactcggtccttaaatgcga---ttacagtctaacatgtgctt-----ttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCACTGGGGCGGTCGACGGAAAATG
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 4
atgatcaaatatttgagcctatcataacttgcatcttcaatttcatgtacatttcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA
|| | ||| |||| | | | | | || ||| || || ||| |||| ||||| ||||||||||| ||||||||||||||| | | || || |||||||| ||||| || || || || || || | || | || ||
----------------------------------------------gtttggt-ccttaaatgcaa---ttacagtctaacatgtgctt-----ttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCGCTGGGGCGGTCGACGGAAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtacatttcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA
ggctaat putative branch site (score: 3)
ttttctgtctt putative PPT
taatacttgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgatcaaatatttgagcctatcataacttgcatcttcaatttcatgtacatttcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - -cttgcat
- - - - - - - - - - - - - - - - - - - - - tcatgta