Sequence
atgc intronic sequence ATGC exonic sequence...aagtttaatgtgaatgtaaactgccttgatcagttttaaatagaaaacaacatatatccattttccctctcccatcacaagttcttgttatctggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAAGGCTGGTTCAGCATCACCAGTTAGTGGATCAG
Basic information
species | Glycine max |
transcript | GLYMA20G35260.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 5
aagtttaatgtgaatgtaaact--gccttgatcagttttaaatagaaaacaacatatatccat-tttccctctcccatcacaag-ttcttgttatctggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAA---GGCTGGTTCAGCATCACCAGTTAGTGGATCAG
| || || | ||| | | |||| | | | | | | | ||| || ||| | ||||||| | ||||| ||| ||||| |||||||| ||||||||||| |||| ||||| ||||| |||||||| || ||| |||| ||||| |||||| |||| || || || ||||| |
----tctattctcttgcatacttggtgtgtatcacccgttatttactagcttttcttgttcatgctttcctattagatcacaaaatgtttgttctctttgccagGTGAGAGATGAACTTGAACAATTATTGGACGATGACGATGACATGGCTGATCTTTACTTGTCCAGAAAGTTGGCTGGGGCAGCTTCCCCTGTCAGTGGCT---
upper sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G159295_T01 (Zea mays), 3'ss of exon 5
--aagtttaatgtgaatgtaaactgccttgatcagttttaaatagaaaacaacatatatccattttccctctcccatcacaagttcttgttatctggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAA---GGCTGGTTCAGCATCACCAGTTAGTGGATCAG
||| ||| | | | ||| ||| || | | || | | | || | | | ||||||| | || | | | ||||| |||||||||||||||||||| ||||||| || ||||| |||||||| || || |||| ||||| |||||| || | || || || ||||| |
ttttatttcatgacattagtattcttggtgaatagtgatagactactagcaccgtttctct-tcgtggtttaggaatcacaaactgttctctgtttgc-cagGTGAGAGATGAGCTTGAACAATTATTGGATGACGACGATGACATGGCTGATCTTTATTTGTCTAGAAAGTTGGCTGGGGCATCTTCCCCTGTCAGTGGTT---
upper sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G09720.1 (Arabidopsis thaliana), 3'ss of exon 5
---aagtttaatgtgaatgtaaactgccttgatcagttttaaatagaaaacaacatatatccattttccctctcccatcacaagttcttgttatctggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAAG---GCTGGTTCAGCATCACCAGTTAGTGGATCAG
| | | || | | | || | | | | | | | | || ||| |||| || | ||| | | ||| | | |||||||||||||| ||| |||| ||||| || ||||||||||| || ||||| ||||| ||| || ||| || | ||||||| || || |
caaagactcattgaaagaaccatcaaaactggagtatatgcttttgggattataccgagtgaaagttgggtctaa-atcagaatatgatgtggatt--tgcagATAAAGGATGAGCTTGAACAGTTGTTGGAAGATGACGAAGATATGGCTGAACTCTACCTTTCAAGGAAGCTCGCGGGTGCATCTTCACCAGCTATTGATT---
upper sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------aagtttaatgtgaatgtaaactgccttgatcagttttaaatagaaaa-caacatatatccattttccctctcccatcacaagttcttgttatc-----tggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAAG---GCTGGTTCAGCATCACCAGTTAGTGGATCAG
| | || | ||| | | || | | | | | || | | | ||| ||||| | | | | | | | || | | ||||| || |||||||||||||| ||| |||||||||||| |||||||||||| || ||||| |||| ||| | |||| || | ||| | || || | |
gtgagtatgtttcactggtaaacagagtctatgtttagaacttgtgttgccacatatactatgagtatgaagcttcctcacatatgtcaagtgaacattcaagatatacgatagtggaacagagaagaattaatctctctcgtcgcttttttttcagGTAAGGGATGAGCTTGAACAGTTGTTGGATGATGATGGTGATATGGCTGATCTCTACCTTACAAGGAAGCTTGTTGGTGCATCTTCATCTGTCAGCGTTT---
upper sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G64560.1 (Arabidopsis thaliana), 3'ss of exon 6
aagtttaatgtgaatgtaaactgccttgatcagttttaaatagaaaacaacatatatccattttccctctcccatcacaagttcttgttatctggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAAGGCT---GGTTCAGCATCACCAGTTAGTGGATCAG
|| | | ||| | | || | || | | || || | | | | | | | | | | || | ||||| |||||||| || ||||| |||||||||||||| ||||||||||| || || ||||| ||||| || | || | | ||||| ||||| |
-------gtgagcaggtatctttttcttatgacttatgagtatttgtaaa---gtttgtaatatgaatagagaactaagtagcttcatcgccttttgcagGTAAGAGATGAACTCGAACAGTTGCTGGATGATGACGATGATATGGCAGATCTTTACCTTTCAAGGAAACTTTCAAGTGCTTCCTCACCGATTAGTAGTA---
upper sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 5
aagtttaatgtgaatgtaaactgccttgatcagttttaaatagaaaacaacatatatccattttccctctcccatcacaagttcttgttatctggt-acagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAA---GGCTGGTTCAGCATCACCAGTTAGTGGATCAG
| ||| | | | || | || | | | | | | || | | | ||| | | | | || ||| | ||||| || ||||||||||||||| | |||||||||||||||||||||||||| || || ||||| ||||| ||||||| || | ||||||||||| || |
acattttccatcagcagcagttga-tcaattatctgctcaatttgtatgcttcacagccttaacactaaagacttcatatggtgctcataactgattgcagGTGAGGGATGAGCTTGAACAACTTCTGGATGATGATGATGATATGGCTGATCTTTATCTGTCCAGAAAATTGGCTGGTGCATCTTCACCAGTTAGCGGCT--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacaacatatatccattttccctctcccatcacaagttcttgttatctggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAAGGCTGGTTCAGCATCACCAGTTAGTGGATCAG
atatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagtttaatgtgaatgtaaactgccttgatcagttttaaatagaaaacaacatatatccattttccctctcccatcacaagttcttgttatctggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAAGGCTGGTTCAGCATCACCAGTTAGTGGATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA