Sequence
atgc intronic sequence ATGC exonic sequencegtatctttgaacagtttggagtgcaattcgttcctctggttttagaaattgattcattattttatcttgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT
Basic information
species | Glycine max |
transcript | GLYMA14G29810.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
gtatctttga-acagtttggagtgcaattcgttcctctggttttag--aaattgattcattattttatcttgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT
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gtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10
----------------gtatctttgaacagtttggagtgca-attcgttcctctggttttagaaattgattcattattttatcttgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT
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gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatc-ttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 10
---------------gtatctttgaacagtttggagtgcaattcg---ttcctctggttttagaaattgattcattattttatcttgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT
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gtatgctagtctatcacattatcaaataga--gcaatatattcagaactttacctgactcttgcttccaattgatc-ttttatcttacagGGAATAATTGTGATGGCTGCAACAAACTTGGCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10
-------gtatctttgaacagtttggagtgcaattcgttcctctggttt------------tagaaattgattcattattttatct-tgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT
| | || ||| | || ||| |||| || |||| ||| | || | |||||| | || ||||||||||| | |||||||||||||||||||||||||| ||||| |||||| | || || || || ||||||||| | |||
gtacttgttgattaggagtagtgtatcttgtgattacttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 10
gtatctt-tgaacag-tttggagtgcaatt---cgttcctctg-gttttagaaattgattcattattttatcttgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT
||| | | || ||| ||| | | | || |||| |||| || | | |||||| |||||||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||||| || ||||| |||||||| |||||
gtaacatatggacaaacttgtgttattagtgaatatttttctgcatttttttaacttggataatatttt-tcttgtagGGCATAATATTGATGGCAGCAACAAACTTGCCTGATATTCTTGATCCAGCTTTAACAAGACCTGGTAGATTTGACAGGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggagtgcaattcgttcctctggttttagaaattgattcattattttatcttgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT
aattgat putative branch site (score: 4)
ttttatctt putative PPT
ttttagaaattgattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctttgaacagtttggagtgcaattcgttcctctggttttagaaattgattcattattttatcttgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA