Sequence
atgc intronic sequence ATGC exonic sequence...gaaacttgaacctacatgttgttcgaagccaattattatgcaattatgcatttccagagttgagggactaaatggttcctttgtttataatttttggtcaGGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCAT
Basic information
species | Glycine max |
transcript | GLYMA18G14620.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G14620.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
------------gaaacttg-aacctacatgt--tgttcgaagccaattattatgcaattatgcatttccagagttgagggacta------aatggttcctttgtttataatttttggtcaGGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCAT-
| | || |||| ||| || | | | | | | |||||||| | |||| | | | | ||||| | | | | ||| | ||||||||||| |||| || | || || || ||||| ||||||||||||||||||| ||||| ||||||||||| ||||||||||| |
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaagtgcatttcaaatgttgtgaaattcttccccactggttattctaat-gtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
upper sequence: GLYMA18G14620.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G396856_T02 (Zea mays), 3'ss of exon 3
-gaaacttgaac----ctacatgttgttcgaagccaattattatgcaattatgcatttcc----agagttgaggga---ctaaatggttccttt--gtt--tataatttttggtcaGGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCAT-
| || | || | ||| | | | ||||||| || | | | | | || || | || | | ||| ||| | | || | ||||||| |||| | || || | ||||||||||||||| || |||||||||| ||||| ||||| ||||| || || |||||||||| |
gtatttttcagtgttacttcttgtcatgtttgtgtgttggtgatgcaatcatatttatttgagaaaaatggaaagatccttttgtgatgcatttcggttgctctgatgcatt-tcagGTTATTCTTCTGGAATCTCGTGATAGAATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCAGTCGATTTGGGAGCATCTTG
upper sequence: GLYMA18G14620.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
gaaacttgaacctacatgttgttcgaagccaattattatgcaattatgcatttccagagttgagggactaaatggttcctttgtttataatttttggt---caGGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCAT-
| || |||| || | |||| |||| || | || ||| | || || | | || ||||| ||||| | | | ||||| | || ||||||||||| ||| |||||||||||||||||||||||||||||||||| || || |||||||
-----------gtttgtgatgttt-----catgttttatacaat---atatcctgatagctgattttgatatctctttctcacggtgtggttcttggtgtttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
upper sequence: GLYMA18G14620.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 2
gaaacttgaacctacatgttgttcgaagccaattattatgcaattatgcatttccagagttgaggg-actaaatggttc-ctttgtttataat-ttttggtcaGGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCAT-
| | || || ||| || | || ||| | | | |||| || | ||| || | || | | | | || | |||||||||| || || || | |||||||||||||| || |||| |||||||||||||||||||||||||||||||||||||||||||
--tagccatagataaatattgctctgttctgtttgctattt--tcgtttttgatcagatttctgtttgctatattcctaactatacacactttatcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcatttccagagttgagggactaaatggttcctttgtttataatttttggtcaGGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCAT
gactaaa putative branch site (score: 2)
ttttt putative PPT
tttgtttataattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaacttgaacctacatgttgttcgaagccaattattatgcaattatgcatttccagagttgagggactaaatggttcctttgtttataatttttggtcaGGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - cttgaac
- - - - - - - catgttg
- - - - - - - - - - - - - - - - - - tatgcaa
- - - - - - - - - - - - - - - - - - - - - - - -gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgagg