Sequence
atgc intronic sequence ATGC exonic sequence...atatatacacacacacacacacacatacatgggggattgttcacacttattatgaaatgtatgttattgaattttttctaattctaatgaatgtcactagGAGCTCATATTGGACCAGAGCCAACAACTGATAGGTTTGTTGTTGTCATG
Basic information
species | Glycine max |
transcript | GLYMA18G10150.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 9
---------atatatacacacacacacacacacatacatgggggattgt---tcaca----cttattatgaaatgtatgttattgaattttttctaat-tctaatgaatgtcact---agGAGCTCATATTGGACCAGAGCCAACAACTGATAGGTTTGTTGTTGTCATG
|| | | | || | | ||| | | || ||| || | | | || || | | ||| ||| | | || || ||| ||||||||||| |||||||| |||||||| || ||||||||| | |
gtaaacaggatgaaatattgtgttccttttccttcttattgagaattatattttccattctctttctacacattttcccttgaaaaaaatgtaacaatatctgagttgtttctcttgcagGTGCTCATATTGGTCCAGAGCCTACAACTGACAGATTTGTTGTTATTACT
upper sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 9
atatatacacacacacacacacacatacatgggggattgttcacacttattatgaaatgtatgttattgaattttttctaattctaatgaatgtcac-tagGAGCTCATATTGGACCAGAGCCAACAACTGATAGGTTTGTTGTTGTCATG
| | ||| ||| | || ||| | |||| | | |||| | | || | || || | ||| | ||| ||||||||||| |||||||| ||||| || ||||||||||| |||
--gtgaa-acaataacatggat-cacccattgttc-ttgtatcccatcattactttgaacaaact-ttaatttaccagtatctgcaatactccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
upper sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 9
-------------------------------atatatacacacacacacacacacatacatgggggattgttcacacttattatgaaatgtatgttattgaattttttctaattctaatga----atgtcactagGAGCTCATATTGGACCAGAGCCAACAACTGATAGGTTTGTTGTTGTCATG
| | | || ||| | | | | || | | | | || | | ||| | ||| | ||| || | |||||||||||||||||||||||| || ||||| || |||||||||||||||
gcaagttatccatcttatcctatcttcttctccttctgtgacctaactagtttcgatattttaaaaagtatgggaacaggtcaatgattaaccgtaaaacagctttatataacttcaattgtcatattttttcagGAGCTCATATTGGACCAGAGCCGACTACTGACAGATTTGTTGTTGTCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttattatgaaatgtatgttattgaattttttctaattctaatgaatgtcactagGAGCTCATATTGGACCAGAGCCAACAACTGATAGGTTTGTTGTTGTCATG
ttctaat putative branch site (score: 2)
aaatgtatgttattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatatacacacacacacacacacatacatgggggattgttcacacttattatgaaatgtatgttattgaattttttctaattctaatgaatgtcactagGAGCTCATATTGGACCAGAGCCAACAACTGATAGGTTTGTTGTTGTCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - acacaca
- - - - - - - - - - - - - - - gggggat
- - - - - - - - - - - - - - - - - - - -ttcacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgt