Sequence
atgc intronic sequence ATGC exonic sequence...acgtgactttgacatatacttgaatattattatccatggtttagtatgttatgttgctgttgtattatggatgtctgattttttagatgtgatgccacagATTTGACCAATGTTCAATCTCTCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACAGTTGTGCAGGAGGCTACTCTTCCAGTAATT
Basic information
species | Glycine max |
transcript | GLYMA16G02880.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G156158_T01 (Zea mays), 3'ss of exon 1
--------acgtgactttgacatatacttgaatattattatccatggtttagtatgttatgttgctgttgtattatggatgtctgattttttagatgtgatgccacagATTTGACCAATGTTCAATCTCTCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACAGTTGTGCAGGAGGCTACTCTTCCAGTAATT
| | | | || || ||| | | |||| | || | |||| | ||| || | || ||| ||| ||||| ||||| |||||| | || |||||||||||| | |||| |||| |||||||||||||||| ||||| ||||||||||||||||| ||| |||||
tactggctgcattgttactgtgcaagtgtgcattttaactattaggagttaggac-ccatcatcctgtagcttta---atagtcagctgtt---atgc-atgtcacagGTTTGATCAATGTGCCATTTCTCCACTGTCACTGAAAGCCATCAAAGATGCTGGATATGAGAGGATGACTCGGGTGCAGGAGGCTACTCTGCCAATAATT
upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G08610.1 (Arabidopsis thaliana), 3'ss of exon 1
acgtgactttgacatatacttgaatattattatccatggtttagtatgttatgttgctgttgtattatggatgtctgattttttag-atgtgatgccacagATTTGACCAATGTTCAATCTCTCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACAGTTGTGCAGGAGGCTACTCTTCCAGTAATT
|| | || | | | ||| || ||| | || || | ||| | || ||| ||| | | | || | |||||||||| |||| || ||||||| | || |||||| |||||||||| |||| ||||| |||||| ||||||||||||||||||||||| | |||
-------------gtaca-ttatttttcactat--gtgacttactttgaccatttagttctgtttgattgataatattctttatggtacatggt-ttacagATTTGATCAATTCCCACTCTCTCCCTTATCGCTAAAAGCCATCAAGGATGCGGGATTTGAGACAATGACTGTTGTGCAGGAGGCTACTCTTCCTATCATT
upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G63630.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------acgtgactttgacata--tacttgaatattattatccatggtttagtatg--ttatgttgctgttgtattatggatgtctgattttttagatgtgatgccacagATTTGACCAATGTTCAATCTCTCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACAGTTGTGCAGGAGGCTACTCTTCCAGTAATT
|||| ||||| || || | || ||| | || || | | || | || | ||| | | | || || | | | | |||||||||| || | | || | ||||| | || |||| | | |||||||||||||||| |||| |||||| ||||| ||||| |||||||| || |||||
gtaaacaaacattgttgcaaatctagtttcttctgtgtgattttgaattaatcacatcaaccttaagagttttgcttgattgtgaatcttgacctcttggtactgtcagattgagagttactcttttcggt-taacagATTTGATCACTATCCATTGTCTCCCTTATCGCTAAAGGCAATCAAGGATGCTGGATACGAGACAATGACTGTTGTTCAGGAAGCTACTCTCCCTATAATT
upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 1
acgtgactttgacatatacttgaatattattatccatggtttagtatgttatgttgctgttgtattatggatgtctgattttttag--atgtgatgcc-acagATTTGACCAATGTTCAATCTCTCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACAGTTGTGCAGGAGGCTACTCTTCCAGTAATT
|||| | | | | | || | || | | | || || ||| | || | | | ||| | | | || | | |||||||||| || | || | ||||| | | ||||||||| | |||||||||||| | ||| |||||| ||||| ||||||||||||||||| | |||
---------gtacattttttgcgtttctttcggagatagcttcagagctattcttagtggtgtttgattcagatttctctttatggtaaaatggttcttacagATTTGATCAGTTCCCACTGTCTCCCTTAACGTTAAAAGGAATTGAGGATGCTGGATTTAAGACAATGACTGTTGTTCAGGAGGCTACTCTTCCTCTCATT
upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g01010.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------------------------------------acgtgactttgacatatacttgaatattatt--atccatggtttagtatgttatgttgctgttgtattatggatgtctgattttttagatgtgatgccacagATTTGACCAATGTTCAATCTCTCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACAGTTGTGCAGGAGGCTACTCTTCCAGTAATT
| | || || | || | | ||| | |||||| | ||| | ||||| | | ||||| || || | || ||| ||||| |||||| ||||||||||| |||||||||||| | |||| ||||| || |||||||| ||||| || || |||||||| || ||||| || ||
gtatgtctactcaaaacacttcttttcggtttttgattaattgtattgaaataggaaagaacgcagaattatggagaaatggtggttagaatgcaaaccaattgagcaaaggtttaacttctatgggaattatggttacaaaggtttaagggttgttgcct---aaacatctgacttccatga-atattg--gcagGTTTGATCAATGTCCAATCTCTCCATTGTCATTAAAAGCAATCAAAGATGCAGGGTATGAGAAGATGACTGTGGTTCAGGAGGCAACCCTTCCTGTCATCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|20498840|gb|BQ273770.1|BQ273770EST: AGACCTTCTTCCCCTGGAGGAGGATCTGATTCTTATTTAAGTGAAACCAG ATTTGACCAATGTTCAATCTCTCCACTGTCATTAAAAGGAGTCAAGGATGC
genomic: AGACCTTCTTCCCCTGGAGGAGGATCTGATTCTTATTTAAGTGAAACCAGgtgtgttcaa ... gatgccacagATTTGACCAATGTTCAATCTCTCCACTGTCATTAAAAGGAGTCAAGGATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttatgttgctgttgtattatggatgtctgattttttagatgtgatgccacagATTTGACCAATGTTCAATCTCTCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACAGTTGTGCAGGAGGCTACTCTTCCAGTAATT
gtctgat putative branch site (score: 4)
attttttagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acgtgactttgacatatacttgaatattattatccatggtttagtatgttatgttgctgttgtattatggatgtctgattttttagatgtgatgccacagATTTGACCAATGTTCAATCTCTCCACTGTCATTAAAAGGAGTCAAGGATGCTGGATATGAGAAAATGACAGTTGTGCAGGAGGCTACTCTTCCAGTAATT
- - gactttg
- - - - - - catatac
- - - - - - - - - - - - - - - - -ccatggt
- - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatgt