Sequence
atgc intronic sequence ATGC exonic sequencegttttactcaggaccccatcaccttgctgtgcttgttacaaagtatttcataatattgaccattttaaaactccagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
Basic information
species | Glycine max |
transcript | GLYMA19G05360.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 4
gttttactcaggacccc--atcacctt---gctgt--gcttgtt--acaaagtatttcataatattgac--cattttaaaactccagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
|||| | | || | | | || | | | ||| || |||| | | | | ||| | | | ||||| |||||||||||||| || | | ||||||||||||||||| || |||||||||||||| || || || ||||| || ||||| |||||||| ||||
gtttgtgttaaaactgctgactagttttaggatataaacttattctgttgagtaatatgtgttctcttttgcataatcatgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGATGCATTTTGGTTATTAGTTGCTTTGCTGAAGGGAGCTGTTCATGCGCCAA
upper sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
gttttactcaggaccccatcaccttgctgtgcttgttacaaagtatttc----ataatattg-accattt-taaaactc------cagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
||| | | | | |||| | | | | || | | || |||||||| | ||| | || || ||||| |||||||||||||| ||||| ||||||||||||||||||||||||||||||| ||||| || || || |||||||| ||||| || ||||| ||||
-gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
upper sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 4
---gttttactcaggaccccatcaccttgctgtgcttgttacaa--agtatttca-taatattgaccattttaaaa-ctccagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
| || | | || | | || || | ||||| | ||| ||| | ||| ||| | || ||||| ||||| ||| |||| || | |||||||| |||||||| || || ||||| || ||||| || || ||||| || |||||||| |||||||||||||
gtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatctgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
upper sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 4
gttttactcaggaccccatcaccttgctgtgcttgttacaaa--gta----tttcataatattgaccattttaaaactc---cagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
|| || | || | || | | ||| | | ||| || | || | | | | ||||| | ||||| ||||| || |||| || | ||||||||||||||||| || || |||||||| ||||| || || ||||| || |||||||| || || | ||||
gtatttccagagatcttttcctttattcttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA
upper sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
gtttta--ctcagg-accccatcaccttgctgt--gcttgttacaaagtatttcataatattgacc----att-ttaaaactccagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
|||| |||| | | | |||||| | || | || || | || | || | |||| || || || | ||||| |||||||||||||| || | ||||||||||||||||||| || |||||||| |||||| |||| ||||| || |||||||| |||||||||||||
gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttgctgtgcttgttacaaagtatttcataatattgaccattttaaaactccagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
tattgac putative branch site (score: 2)
tatttcataatattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttactcaggaccccatcaccttgctgtgcttgttacaaagtatttcataatattgaccattttaaaactccagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG