Sequence
atgc intronic sequence ATGC exonic sequence...gttgcttttgtataactcgctggttatgctataaattattgtctgaaatttatgctgtatttgcaattacctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGGATTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
Basic information
species | Glycine max |
transcript | GLYMA10G33830.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g41370.1 (Oryza sativa), 3'ss of exon 2
--gttgcttttg-----tataactcgctggttatgctat-aaattattgtctgaaatttatgctgtatttgcaattacctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGGATTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
||| | | || | || || ||| | || | | || |||| | | ||| || |||| | | | || | || | ||| ||| | ||||||| |||||||| || || || |||||||| |||||||| ||||||||||||||||||||| | |||| ||| | ||||| || ||||| ||||
gggttcatctcaacggatactaatctcttgttctactcttatgttgttgttagcagttt---ttggatttaaactgat---aatcctaagaac--atgattgtcacagGTTCTGATATATTCACCGGATGGGAGGTGCCTGTTCAAGTACTTAGCATATGAAAGTGGATTAGGTGTGAAAACTGTTGCGTGGTCACCATGTGGACAGT
upper sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G374969_T01 (Zea mays), 3'ss of exon 2
gttgcttttgtataactcgctggttatgctataaattattgtctgaaatttatgctgtatttgcaa-ttacctaaaacttagtcatttatgttt------gatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGGATTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
| | | |||| || |||||| | | | | || ||| || || || ||| ||| | || | | ||| | | ||| || ||||||| |||||||| ||||||||||||||| | |||||||||| ||| ||||||||||| || || | |||| ||| | ||||| || ||||| ||||
-taaactaagaataatacg---attatgcaaaga--tgctaactacaatg-attctttaagaacaaattatttcaagttctgacatctttctttttgtcacttacagGTTCTGATATATTCGCCAGACGGAAGGTGCTTGTTCAAGTATCTAGCTTATGAAAGTGGGTTGGGTGTGAAAACTGTTGCTTGGTCACCATGTGGACAGT
upper sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G07590.1 (Arabidopsis thaliana), 3'ss of exon 2
gttgcttttgtataactc-gctggttatgctat----aaattattgtctgaaatttatgctgtatttgcaattacctaaaacttagtcatttatg--tttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGGATTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
| ||||| | | | | ||||||| | || || | ||| ||| | ||| | || | | || |||| | ||| |||||||||| ||||||||||| || ||||| || || ||||| || ||||||||| ||||| | || | || | ||| ||||||||||| ||||||||||
-----gtatgtatcgttttggtattgatgctatttttagatagttattggaattttgttatgtttggtttgttggagatatctctaaaatttgtaccttttgggcagGTTCTAATTTATTCTCCAGATGGTAGGTGTCTGTTTAAGTACCAGGCATATGAATGTGGACTTGGTGTCAAGACTGTTTCCTGGTCTCCGTGTGGTCAGT
upper sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 3
gttgcttttgtataactc--gctggttatgctataaattattgtctgaaatttatgctgtatttgcaattacctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGGATTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
|| ||| ||| | ||| || || || | | | || ||| || || || | | | || ||||| || ||||||| || || || ||||| || |||||||| | |||||||||||||||||||||||| |||| | || | || || |||||||||||||||||||
--tgatttgtgatattttaagcttcagatactgtacagttgtagtgacaaactattcttggttgaaaaatgaaaagcttaaaatctgcatggtttggtacagGTTCTTATCTACTCCCCAGATGGGAGGTGCCTATCTAAGTATCAAGCATATGAAAGTGGACTAGGTGTGAAGACCGTTTCATGGTCTCCTTGTGGTCAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatttatgctgtatttgcaattacctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGGATTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
atttatgtttgatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgcttttgtataactcgctggttatgctataaattattgtctgaaatttatgctgtatttgcaattacctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGGATTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
gttgctt
- - - - - - - - - gctggtt
- - - - - - - - - - - - - tgctata
- - - - - - - - - - - - - - - - - - - ttgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgcaa