Sequence
atgc intronic sequence ATGC exonic sequencegtataatgctcaaattttctattactgtttctgaaaattaaaatttacttttggtttctgaccgttggttaatttgcctttccccttttcagAAGAAGTCATTGGCCATGTTCCAGCATGATTCAAATTGTATGGCACTTCTGATGGATGGAAGTGCTGCATTGGGTCTTGATTTGAGTTTTGTTACGCATG
Basic information
species | Glycine max |
transcript | GLYMA04G28970.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G28970.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g72310.1 (Oryza sativa), 3'ss of exon 5
------------------gtataatgctc-aaattttctattactgtttctgaaaattaaaat--ttacttttggtt---tctgaccgttggttaatttgcctttcccctt-ttcagAAGAAGTCATTGGCCATGTTCCAGCATGATTCAAATTGTATGGCACTTCTGATGGATGGAAGTGCTGCATTGGGTCTTGATTTGAGTTTTGTTACGCATG
|| || || | | | | | | ||| ||| | || | || |||||| | || | |||||| | |||| | ||| || | | |||| | ||||| || || ||||| | | |||||||||| ||| ||| |||| ||||||||||||||||| | |||
gtacgttttacaatttattcatcctgttccacactgccctctgttccctctttaaaatgaactgcctatttttggggaaactatgctaatgtggattttgccacaattataacgcagAGAAGTTCACTGACGAAGTTCAAAGATGATCCAGCATGCATGGCCTTAGTCATGGATGGAACTGCAGCACTGGGCCTTGATTTGAGTTTTGTCTCTTATG
upper sequence: GLYMA04G28970.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G54460.1 (Arabidopsis thaliana), 3'ss of exon 5
gtataatgctcaaattttctattactgtttctgaaaattaaaatttacttttggtttctgaccgttggttaatttgcc-tttccccttttcagAAGAAGTCATTGGCCATGTTCCAGCATGATTCAAATTGTATGGCACTTCTGATGGATGGAAGTGCTGCATTGGGTCTTGATTTGAGTTTTGTTACGCATG
|| | || | | | | | ||||| | | | | | || | || || || | |||| ||||||||| ||| | |||| ||||||||| | ||| | |||| ||||||||| ||||||||||||||| || | |||||||||||||||||||| || ||||
--gtacttgtctgttgatttgtatttctttctcacatcttgcaatcctttataa---------gtcaaacaactttcgatttcaacttttcagATGAAAGCTCTGGCAATGTTCCAGAACGATGCTGATTGCATGGCACTTTTGATGGATGGAAGTGGGGCCCTTGGTCTTGATTTGAGTTTTGTAACACATG
upper sequence: GLYMA04G28970.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g03330.t01 (Vitis vinifera), 3'ss of exon 6
gtataatgctcaaattttctattactgtttctgaaaattaaaatttacttttggtttctgaccgttggttaatttgcctttccccttttcagAAGAAGTCATTGGCCATGTTCCAGCATGATTCAAATTGTATGGCACTTCTGATGGATGGAAGTGCTGCATTGGGTCTTGATTTGAGTTTTGTTACGCATG
| || | || || ||| ||||| | | || ||| ||| || | || | |||||| | | || |||||||| |||||| | ||| |||||||||||| || |||||||||| ||| |||||||||||||||| ||||| || ||||||||||| ||||| || ||||
-----gtactaatataatccatt-----ttctgtatttccaacttt--ctttaaattatttccaa-gattaattcac-tgtcagtttttcagATGAAGTCGCTATCCACCTTCCAGCATGATGCAGATTGTATGGCTCTTTTGATGGATGGAAGTGCAGCATTAGGCCTTGATTTGAGCTTTGTAACACATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaatttacttttggtttctgaccgttggttaatttgcctttccccttttcagAAGAAGTCATTGGCCATGTTCCAGCATGATTCAAATTGTATGGCACTTCTGATGGATGGAAGTGCTGCATTGGGTCTTGATTTGAGTTTTGTTACGCATG
ttaatttgcctttccc CT-rich tract
atttactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatgctcaaattttctattactgtttctgaaaattaaaatttacttttggtttctgaccgttggttaatttgcctttccccttttcagAAGAAGTCATTGGCCATGTTCCAGCATGATTCAAATTGTATGGCACTTCTGATGGATGGAAGTGCTGCATTGGGTCTTGATTTGAGTTTTGTTACGCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC