Sequence
atgc intronic sequence ATGC exonic sequence...tatatgactctgaatatatttgaatcgtattatccatgctttagtatgttatgctgctattgtattatgaatgtctgatttttgagatgtgttgccgcagATTTGACCAATGTTCAATCTCCCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACGGTTGTTCAGGAGGCTACTCTTCCAGTAATT
Basic information
species | Glycine max |
transcript | GLYMA07G06240.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G08610.1 (Arabidopsis thaliana), 3'ss of exon 1
-tatatgactctgaatatatttgaatcgtattatccatgctttagtatgttatgctgctattgtattatgaatgtctgatttttgagatgtgttgccgcagATTTGACCAATGTTCAATCTCCCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACGGTTGTTCAGGAGGCTACTCTTCCAGTAATT
|| || | | | | ||| ||| | || ||| |||||| || || ||| ||| | ||| || | || | ||||||||| |||| || |||| || | || |||||| |||||||||| |||| ||||| |||||| ||||| ||||||||||||||||| | |||
gtacattatttttcac-tatgtgacttactttgacca---tttagtt----------ctgtttgattgataatattc--tttatggtacatggt-ttacagATTTGATCAATTCCCACTCTCTCCCTTATCGCTAAAAGCCATCAAGGATGCGGGATTTGAGACAATGACTGTTGTGCAGGAGGCTACTCTTCCTATCATT
upper sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G63630.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------tatatgactctgaatatatt---tgaatcgtattatccatgctttagtatg--ttatgctgctattgtattatgaatgtctgatttttgagatgtgttgccgcagATTTGACCAATGTTCAATCTCCCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACGGTTGTTCAGGAGGCTACTCTTCCAGTAATT
| | ||| | ||||| || | || | || | ||||| | | || | || | ||| | | | | || || | | | ||||||||| || | | || | || || | || |||| | | |||||||||||||||| |||| |||||| ||||||||||| |||||||| || |||||
gtaaacaaacattgttgcaaatctagtttcttctgtgtgattttgaattaatcacatcaaccttaagagttttgcttgattgtgaatcttgacctcttggtactgtcagattgagagttactcttttcggt-taacagATTTGATCACTATCCATTGTCTCCCTTATCGCTAAAGGCAATCAAGGATGCTGGATACGAGACAATGACTGTTGTTCAGGAAGCTACTCTCCCTATAATT
upper sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 1
-tatatgactctgaatatatttgaatcgtattatccatgctttagtatgttatgctgctattgtattatgaatgtctgatttttgagatgtgttgccgcagATTTGACCAATGTTCAATCTCCCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACGGTTGTTCAGGAGGCTACTCTTCCAGTAATT
|| || | || | | ||| || || ||| | | || || | || | | | ||| | | | ||| ||| ||||||||| || | || | || || | | ||||||||| | |||||||||||| | ||| |||||| ||||||||||||||||||||||| | |||
gtacatt-ttttgcgtttctttcggagatagcttcagagctattcttagtggtgtt-----tgattcagatttctctttatggtaaaatg-gttcttacagATTTGATCAGTTCCCACTGTCTCCCTTAACGTTAAAAGGAATTGAGGATGCTGGATTTAAGACAATGACTGTTGTTCAGGAGGCTACTCTTCCTCTCATT
upper sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g01010.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------------------------------------tatatgactctgaatatatttgaatcgtatt--atccatgctttagtatgttatgctgctattgtattatgaatgtctgatttttgagatgtgttgccgcagATTTGACCAATGTTCAATCTCCCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACGGTTGTTCAGGAGGCTACTCTTCCAGTAATT
| | | | | | ||| | | ||| | ||| || | ||| | | ||| | || ||||| || || | ||| |||| ||||| |||||| ||||||| ||| |||||||||||| | |||| ||||| || |||||||| ||||| || ||||||||||| || ||||| || ||
gtatgtctactcaaaacacttcttttcggtttttgattaattgtattgaaataggaaagaacgcagaattatggagaaatggtggttagaatgcaaaccaattgagcaaaggtttaacttctatgggaattatggttacaaaggtttaagggttgttgcct---aaacatctgacttccatga-atattg--gcagGTTTGATCAATGTCCAATCTCTCCATTGTCATTAAAAGCAATCAAAGATGCAGGGTATGAGAAGATGACTGTGGTTCAGGAGGCAACCCTTCCTGTCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttatgctgctattgtattatgaatgtctgatttttgagatgtgttgccgcagATTTGACCAATGTTCAATCTCCCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACGGTTGTTCAGGAGGCTACTCTTCCAGTAATT
gtctgat putative branch site (score: 4)
tattgtattatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatatgactctgaatatatttgaatcgtattatccatgctttagtatgttatgctgctattgtattatgaatgtctgatttttgagatgtgttgccgcagATTTGACCAATGTTCAATCTCCCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACGGTTGTTCAGGAGGCTACTCTTCCAGTAATT
- - - -ctctgaa
- - - - - - - - - - - - - - - - -ccatgct
- - - - - - - - - - - - - - - - - - - - - - - - - atgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgt