Sequence
atgc intronic sequence ATGC exonic sequencegtgtgttgatttttattcctgtgagttggtaaatcttgcttttggaagacacccgagttggaagttcaaattctgtttttgacatgcagCTTCCTGATTATCATGATGTGATCGAGCATCCCATGGACTTTGCCACTGTGAGGAAGAAGTTGGGAAATGGATCTTATACTACCTTAGAACAATTTGAG
Basic information
species | Glycine max |
transcript | GLYMA13G05000.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G05000.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G044044_T01 (Zea mays), 3'ss of exon 4
--gtgtgttgatttttattcctgtgagttggtaaatcttgct-tttggaagacacccga--gttggaagttcaaattctg-tttttgac--atgcagCTTCCTGATTATCATGATGTGATCGAGCATCCCATGGACTTTGCCACTGTGAGGAAGAAGTTGGGAAATGGATCTTATACTACCTTAGAACAATTTGAG
| | || || ||| | || | || | | |||| | || |||| || | || || || |||| | ||||| |||||||||||||||||||| ||||| || |||||||| | ||| || ||||||||| | | | | ||| | || || |||||||||
gtaagagcccatattcatttcccatgcttcctggatttgccaatttgtttggtacggagctgttgagtattaatatcgtggttattgattgacacagCTGCCTGATTATCATGATGTGATTGAGCACCCAATGGACTTCGGCACCGTCAGGAAGAAGCTTGCCAGGAATGCATATCGCTCGTTTGAGCAATTTGAG
upper sequence: GLYMA13G05000.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 4
gtg-tgttgatttttattcctgtgagttggtaaatcttgcttttgga--agacacccgagttggaagttcaaattctgtttttg------acatgcagCTTCCTGATTATCATGATGTGATCGAGCATCCCATGGACTTTGCCACTGTGAGGAAGAAGTTGGGAAATGGATCTTATACTACCTTAGAACAATTTGAG
|| || || ||| | | | | | || | | ||| || || | ||| | ||| | | ||||||||||||||||||||||| |||| |||||||||||||| ||| |||| |||||||||||| | | |||||||| ||| |||| || ||| | | |||
gtaatggtggatttcctggagttatctctgaccaatctgttccgaaattagagttttaagctgttttatttgatttttctttgggattgtatttgcagCTTCCTGATTATCATGATATGATAGAGCATCCCATGGATTTTTCCACAGTGAGGAAGAAGCTTGCGAATGGATCATATTCTACGTTGGAAGAGCTCGAG
upper sequence: GLYMA13G05000.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0090g00610.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgttgatttttattcctgtgagttggtaaatcttgcttttggaagacacccgagttggaagttcaaattctgtttttga-catgcagCTTCCTGATTATCATGATGTGATCGAGCATCCCATGGACTTTGCCACTGTGAGGAAGAAGTTGGGAAATGGATCTTATACTACCTTAGAACAATTTGAG
|||| | | | | || | | ||| | || | || || | | ||||| || | | ||| || | | | |||| |||||||||||||||||||| |||||||| |||||||| || || ||||||||||| | || ||||| || ||| |||||| || ||||||||
gtgtttgaaat---actctcttaatttgctttatgtaatttgaagacattatttgcattgga-gtctataacttgtgttggttcttatagCTGCCTGATTATCATGATGTGATTGAGCATCCAATGGACTTCGCGACAGTGAGGAAGAAACTTGGGAATGGGTCATATCGTACCTTTGAGGAATTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgcttttggaagacacccgagttggaagttcaaattctgtttttgacatgcagCTTCCTGATTATCATGATGTGATCGAGCATCCCATGGACTTTGCCACTGTGAGGAAGAAGTTGGGAAATGGATCTTATACTACCTTAGAACAATTTGAG
ttttgac putative branch site (score: 3)
ttctgttttt CT-rich tract
ttcaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttgatttttattcctgtgagttggtaaatcttgcttttggaagacacccgagttggaagttcaaattctgtttttgacatgcagCTTCCTGATTATCATGATGTGATCGAGCATCCCATGGACTTTGCCACTGTGAGGAAGAAGTTGGGAAATGGATCTTATACTACCTTAGAACAATTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT