Sequence
atgc intronic sequence ATGC exonic sequence...gtttttagtttgttgtgcatgtgcttctgttgacgctgcttttgaaatattgtttacttttggtttatcttcacttacaagttacatcattctgttgaagCCCAACTGCAAGGAACTACTCAAGATCACCTGCAAATATTTAACATTGAGATGAAAGCAAAGATGAAATCATATCAGATGCCTGAGCAG
Basic information
species | Glycine max |
transcript | GLYMA14G06340.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttttagtttgttgtgc--atgtgcttctgttgacgctgcttttgaaat-attgtttacttttggtttatcttcac--ttacaagttacatcattctgt-tgaagCCCAACTGCAAGGAACTACTCAAGATCACCTGCAAATATTTAACATTGAGATGAAAGCAAAGATGAAATCATATCAGATGCCTGAGCAG
|| || ||| || || | | | ||| | | ||| | | ||| | | ||||||| | | || |||| ||| | | | || ||| ||| | | |||||||||||| ||||| || || |||||||||||||| ||||||||| |||||||| |||||||||||||||||
gtacttgattttttcctttgatctaaaacccataacggtttcctcgaattcgtagttcataatccacttatcttgatgttcactttttacttcaatatttatgtagCTCAAGTTCCAGGAACTACTCAGGATCATCTACAGATATTTAACATTGAAGCCAAAGCAAAGTTGAAATCACATCAGATGCCTGAGCAG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 2
----gtttttagtttgttgtgcatgtgcttctgttgacgctgcttttgaaatattgtttacttt-tggtttatcttcacttacaagttacatcattctgttgaagCCCAACTGCAAGGAACTACTCAAGATCACCTGCAAATATTTAACATTGAGATGAAAGCAAAGATGAAATCATATCAGATGCCTGAGCAG
|||| |||||| || |||| ||| | ||| | | | | || ||| ||| | ||| | || |||| || | ||| | | ||| ||| | | |||||||||||| ||||| || || |||||||||||||| || |||||| |||| ||| |||||||||||||||||
tagaaattttggtttgtactggatgtttccttgtataagctattacttatttcttccttaatttgttgttaactttttctta-aattcgtatcgt----atatagCTCAAGTTCCAGGAACTACTCAGGATCATCTACAGATATTTAACATTGAAGCAAAGGCAAAGTTGAAGTCACATCAGATGCCTGAGCAG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 2
gtttttagtttgttgtgcatgtgcttctgttgacgctgcttttgaaatattgtttacttttggtttatcttc--acttacaagttacatcattctgttgaagCCCAACTGCAAGGAACTACTCAAGATCACCTGCAAATATTTAACATTGAGATGAAAGCAAAGATGAAATCATATCAGATGCCTGAGCAG
|| | | || || || || | | | | ||| || || ||| |||| | || ||| || | |||| | |||||| ||||||| ||||| | ||||| || || |||||| ||||||||||||| |||||||||||||| || |||||||||||||| ||||||||||||
attgtcatttagtagtttcattggtggtctatgtgtcaatttcaaag--ttatttgtttttcatatactttctggctcatgagtttaaacattcttttgaagCTCAACTTCCGGGAACCACCCAGGATCACTTGCAAATATTTAATATTGAGATGAAAGCCAAAATGAAATCATATCAAATGCCTGAGCAG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 2
gtttttagtttgttgtgcatgtgcttc-tgttgacgctgcttttgaaatattgtttacttt-tggtttatcttcacttacaagttacatcattctgttga-agCCCAACTGCAAGGAACTACTCAAGATCACCTGCAAATATTTAACATTGAGATGAAAGCAAAGATGAAATCATATCAGATGCCTGAGCAG
| ||| || | | || || ||| | | || ||| | | || ||||| || || | | | | | | | | ||| | | | | || | || ||||||||| ||||||| |||||||||||| | || || || |||||||| |||||||||| || |||
---tatagattatctttttggtttttgatgtctaagatgtacttgctagaacgtcaactttatgaagtactgatcttggctatgttggtgctctaatcaacagCTCTAATTCCTGGGTCAACGCAAGATCACTTGCAAATTTTTAACATTGAGTTAAAGGCGAAAATGAAATCGCATCAGATGCCAGAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatattgtttacttttggtttatcttcacttacaagttacatcattctgttgaagCCCAACTGCAAGGAACTACTCAAGATCACCTGCAAATATTTAACATTGAGATGAAAGCAAAGATGAAATCATATCAGATGCCTGAGCAG
cacttac putative branch site (score: 2)
tcattct putative PPT
tttactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttagtttgttgtgcatgtgcttctgttgacgctgcttttgaaatattgtttacttttggtttatcttcacttacaagttacatcattctgttgaagCCCAACTGCAAGGAACTACTCAAGATCACCTGCAAATATTTAACATTGAGATGAAAGCAAAGATGAAATCATATCAGATGCCTGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG