Sequence
atgc intronic sequence ATGC exonic sequence...ttatgaatgattttggttatggatgatttttctcaacttctcgtttttgttatttcaatcttattattagtctttcttatcacatatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG
Basic information
species | Glycine max |
transcript | GLYMA11G27200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 1
----ttatgaatgattttggttatggatgatttttctcaacttctcgtttttgttatttcaatcttattattagtctttcttatcacatatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG---
| | ||| || || | | || ||| | ||| ||||| | | | || || || | ||| | | || || || |||||||||||||| ||||| || | |||||||| ||||| || ||||| ||||| ||||| |||||||||||||||||||| || |||| || || |
cttataaccaatagttggctctactattaaacttgctcttatgctcttttttacttgtgagaagttttttataaccaaacttg--ataaatcatttctt--cagGTTCTCTCTGTGGTTGGAATTTTGCAAGATGAGGTTGACCCT---ATGGTTTCTGTCATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCGGACATCGGTG
upper sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 1
-ttatgaatgattttggttatg-gatgatttttctcaacttctcgtttttgttatttcaat-cttatt-attagtctttcttatcacatatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG---
|| |||| | | | | | |||| | | | | || | |||| ||| |||||| | || | | || || | ||| ||||||| || || ||||| || | ||||| ||||||||||| ||||| ||||| ||||| |||||||||||||||||||| || |||| ||| ||||
aaaatcaatgctgctcctcaagtgatgtactctgtgttttatgtacttccttgatttgaatgcttatttagtaaacagcttggccaaatgtttccctt----agGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCT---ATGGTTTCTGTGATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCTGACATTGGTG
upper sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 1
--ttatgaatgatt-ttggttatggatgatttttctcaacttctcgtttttgttatttcaatcttattattagtctttcttatcacatatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG---
| | ||| | || ||| | || | | | ||||| || | | || || || | || ||| | || |||||||||||||| ||||| | | ||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| |||| ||| ||||
tgtgctcaataaccatttgttgtaaattgcacgctttagtggattgttttgaccatcaggagaggttcatcttgtttgctcact-caaatgttcactt--cagGTTCTCTCTGTGGTTGGTATATTGCAAGATGAAGTTGATCCT---ATGGTATCTGTGATGAAAGTTGAGAAAGCGCCTTTGGAATCTTATGCTGACATTGGTG
upper sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 1
--ttatgaatgattttggttatggatgatttttctcaacttctcgtttttgttatttcaatcttattattagtctttcttatcacatatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG---
| || || | | | || || ||||| | | | | || | || | ||| || | || | ||||||||| ||||| ||||| | | ||||||||||||||||| ||||| ||||| ||||| ||||| || |||||||||||||| |||| ||| ||||
tttgttgcattgcacatgcattagtggaccgtttacaactggtaggggatagcaagccagcttgttttctcactcaaacagtcaaatgt--ttactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCT---ATGGTATCTGTGATGAAAGTTGAGAAAGCACCTTTGGAATCTTATGCTGACATTGGTG
upper sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
ttatgaatgattttggttatggatgatttttctcaacttctcgtttttgttatttcaatcttattat-tagtctttcttatcacatatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG---
|| || | | | | | | ||| |||| | ||| | | ||| |||| | || | | |||| ||||||||||||||| |||||||||||||||| |||||| ||||| ||||| ||||| || || ||||| |||||||| ||||||| ||| ||||
---------------gtattgagttttacaatgctcttccatggaaacgttgaaccaattcttctatgtgatattttttattat------ttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCA---ATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG
upper sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 1
ttatgaatgattttggttatggatgatttttctcaacttctcgtttttgttatttcaatcttattattagtctttcttatcacatatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG---
|||| ||| |||| || || || | || | || || ||| | || || | | | | | || || || | | | |||||||||||||||||||| |||| ||||||||||| |||||| ||||| ||||| ||||| ||||| || || |||||||| ||||||| ||||||||
gtatgtgaaattagggtttaaga--atcttgttt---ttgttgtgattacgattgtg-tgttgttgtggatttagggttgctgatttg-ttttatgttagGTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCA---ATGGTGTCTGTGATGAAAGTTGAGAAAGCTCCTTTGGAGTCATATGCTGATATTGGAG
upper sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 1
ttatgaatgattt-tggttatggatgatttttctcaacttctcgtttttgttatttcaatcttattatt-----agtctttcttatcacat-atggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG---
|| ||| | |||||| || || ||| || || | | | ||| |||| | || || || | | ||| || | || | | ||||||||| ||||||||||| ||||| ||||| |||||||||||| ||||| || || ||||| ||||| ||||| || ||||||||||||| ||| || |
-----tctgttttatagttatgcattcttattcaca--ttgaagatgtagttccttcaccatcatagtttcaggaggttcttatattactttgtgctgtctcgtcagGTTCTTTCTGTTGTTGGTCTTCTCCAAGACGAAGTTGATCCA---ATGGTGTCCGTAATGAAAGTTGAGAAGGCTCCATTGGAATCATATGCTGACATAGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttatttcaatcttattattagtctttcttatcacatatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG
ttctttatc CT-rich tract
tatttcaatcttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgaatgattttggttatggatgatttttctcaacttctcgtttttgttatttcaatcttattattagtctttcttatcacatatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCATTAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGTTGATATTG
- -tgaatga
- - - - - - - - - -tggatga
- - - - - - - - - - - - - - - - -caacttc