Sequence
atgc intronic sequence ATGC exonic sequencegtaatagcaaaaaacaactttagtttaatgaacattgtctgtggtgtatggtgttcatcaattggtttttcgatgatgcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG
Basic information
species | Glycine max |
transcript | GLYMA06G03040.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os10g10500.1 (Oryza sativa), 3'ss of exon 13
------------------------------------------------------------gtaatagcaaaaaacaactttagtttaatga----acattgtctgtggtgtatggtgttcatcaattggtttttcgatgatgcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG
| ||| || | | ||||| || | || | || | ||| | ||| | | ||| |||||| ||||| |||| ||| | |||||||| |||||||| ||||| ||||||||||||||||| ||||| || ||| |||| || ||| | ||||||||
gtaagtaagaatcttctatggaatatgccatgattgagttgtatgacaataagattacatatgata-catgatatttttttagaactattatattgttttacttaaaacagtaggccattctcattcagttgtgtaactatgtaacagGTATCAGTTTATTCCTCAGCTGATATTCTTGAACAGCTTATTTGGTTACCTTTCACTCCTCATCATTATTAAGTGGTGCACGGGCTCAAAAGCTGACCTT
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 13
-------------------------------------------------gtaatagcaaaaaacaactttagttta-atgaacattgtctgtggtgtatggtgttcat---caattggtttttcgatg-atgcct--------cagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG
|| | | ||||| | || | | | | || | || | |||| | |||| ||||| | | | ||||||||||||| |||||||| | || ||||| |||||||| ||||||||||| || | ||||| ||||| || ||| |||| ||||| | || || ||
gtaagtttattcaccttttattttatcagacaatatgacattccattttgtgacgaggatctacaacaattgtgaagaagcagtccttcaacagcgtgtttcaatcatatactattgtttttttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------gtaatagcaaaaaacaactttagt-ttaatgaacattgtctgtggtgtatggtgttcatcaattggt-ttttcgatgatgcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG
||| | || || | | | || | | | |||| | | | | || | || | || ||||||||||||| |||||||| | || ||||| |||||||| ||||| ||||| || | || || ||||| || ||| |||| |||||| | || || ||
gtaagtttattcaccttttagcagacaatttgacattccattttgagatgaggactacaacaatcgtgaagaagcatgtgatcctttaacagcgttgttacagacaacagattatgatttttccacgcttactcctttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGTTACCTGTCCTTGCTTATTATTATTAAGTGGTGCACGGGGTCAAAAGCAGATCTA
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 13
----gtaatagcaaaaaacaactttagtt-taatgaacattgtctgtggtgtatggtgttcatcaattggtttttcgatgatgcctc-agGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG
||| | ||| | | | || | | | || || || | | | | || | ||| | || ||| || |||| |||||||||||||||||| |||||||| ||| ||||||||||||| ||||| ||||||| || ||||| ||| ||||||| || || || || |
gtgagtatt--caattttctgcccttgtcattacgtac-ttctcccagttcttcaattatctgcccttgtctgatctcacatggttccagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------gtaatagcaaaaaacaacttt----agtttaatgaacattgtctgtggtgtatggtgttcatcaattggtttttcgatgatgcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG
||||| || | |||| | |||| | | || | ||| || | |||| || ||| |||| ||||||| ||||||| || |||||||| ||||||||||||||||| || ||| ||||||| || ||||| ||| ||||||| || || || || ||
gtgggttcagttgatattttctgaccatagcgtgctctctctctctccagttccttaaacagtaaaaatcagtcatcat-ctcagcatctaattttgcgggcttgc---agGTTCCAGTTCATTCCCCAAATGATATTCTTGAACAGCTTGTTTGGCTATCTCTCAGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTG
upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 13
-----------------gtaatagcaaaaaacaactttagtttaatgaacattgtctgtggtgtatggtgttcatcaattggtttttcgatgatgcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG
|| | | | |||||| ||| | ||| | | | || || | | || | | | |||||||||| || ||||||||||| ||||| ||||||||| | ||||| |||||||| |||||||||||| | |||||| ||| || ||||| ||||| ||
tttttcgttctaaatgtgtgtttgtgcttgagttctttagattatattattgtgttgactattaaggatgcacaatcagcattaatttg-catttcttcagGTACCAATTTGTTCCCCAGATGATATTTTTAAACAGCCTTTTTGGGTACCTTTCTCTCCTCATAATTGTGAAATGGTGCATGGGTTCACAAGCTGATCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacattgtctgtggtgtatggtgttcatcaattggtttttcgatgatgcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG
atcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagcaaaaaacaactttagtttaatgaacattgtctgtggtgtatggtgttcatcaattggtttttcgatgatgcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA