RetrogeneDB ID: retro_gacu_15

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupI:15150060..15151016(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000012245
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GRINA
• Ensembl ID: ENSGACG00000005238
• Aliases: None
• Description: glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding) [Source:HGNC Symbol;Acc:4589]

Sequence

>retro_gacu_15
ATTATGGGTGAGAGCAACCCGCTTCACAACAACATCTATGGACCCCCTCAGCCGGGTTTCGGCATGCCCCCTCCCAACTA
CAGCCAAGCCCCCGGGGAGCCATACCCCCCCGGCAACAGGATACGGACAGCCAGGCTACCTCCAGGCAGGACCGGGCTTC
GCCCCTGGTCCCTACACTCAGATGCCTTATGCTCAGATGCCATGCCCACAGGGACCCTACCCGCAGGGGCCTTATCAGCA
AGGACACCCGCAGCAAGGCTTTCCCGTTGACCCGATGGCTCCTACCGGCAGTCCTGGTTACCATGGCGAGGGGCCTCCAT
ACGATAACGAGGAGTTCAGTGACTCTGGCTTTGAGGACAAGACCATCAGACAAGCATTCATCAGAAAAGTCTTCATGGTT
CTCACGGTGCAGCTGGTTGTCACTTTTTCGTTTGTTGTTGTCTTCACCTTCATCGATGAGGCCAAGTACTTTGTGCGGCG
CAACCCGTGGACATACTATGTGTCCTATGCAGTCTTTTTTTGTGTCTCTGATTGTCCTCAGCTGTTGTGGAGACTTCCGC
CGCAAACATCCCTGGAACTTAGTCGCACTGTCCATTCTGACCCGGAGTCTCTCCTACATGGTGGGCATGATTGCCAGCTT
CTATGACACAGAGACTGTCATCATGGCCGTGGGCATCACTGCAGTCGTCTGCTTCACGGTCGTGCTCTTCTCACTACAGA
GCAAGTATGACTTCACTTCCTGTCGGGGCGAGCTGTTCGTTTGCCTGATTGTGCTGTTGCTCTTCGCCTTTCTCTGCATC
TTCATCCGCCACAGGATCCTTCACATCGCTTATGCCTCACTGGGGGCCCTGCGCTTCACTTGCTTTTTGGCTGTGGACAC
TCCGCTCCTCCTCGGCAACAAGAAGCTGGCTTTGAGTCCAGAGGAGTACGTTTTTGCCTCTACCTCTACACTGACA

Alignment

ORF - retro_gacu_15 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.21 %
• Parental protein coverage: 92.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IMGESNPLHNNVYGPPQPGFGMPPPNYSQAPGEPYPP-ATGYGQPGYPQAGPGFAPGPYPQMPYAQMPYP
          IMGESNPLHNN.YGPPQPGFGMPPPNYSQAPGEPYPP.ATGYGQPGY.QAG....PG..P..PY.QMPY.
Retrocopy IMGESNPLHNNIYGPPQPGFGMPPPNYSQAPGEPYPP>ATGYGQPGYLQAG----PGFAPG-PYTQMPYA

Parental  QGPYPQGPYPQGPYQQGHPQQGFPVDPMAPTGSPGYHGEGPPSYYDNEEFSDSGFEDKTIRQAFIRKVFM
          Q.P.PQGPYPQGPYQQGHPQQGFPVDPMAPTGSPGYHGEGPP..YDNEEFSDSGFEDKTIRQAFIRKVFM
Retrocopy QMPCPQGPYPQGPYQQGHPQQGFPVDPMAPTGSPGYHGEGPP--YDNEEFSDSGFEDKTIRQAFIRKVFM

Parental  VLTVQLLVTFSFVAVFTFVDEAKYFVRRNPWTYYVSYAVFF-VSLIVLSCCGDFRRKHPWNLVALSILTL
          VLTVQL.VTFSFV.VFTF.DEAKYFVRRNPWTYYVSYAVFF.VSLIVLSCCGDFRRKHPWNLVALSILT.
Retrocopy VLTVQLVVTFSFVVVFTFIDEAKYFVRRNPWTYYVSYAVFF>VSLIVLSCCGDFRRKHPWNLVALSILTR

Parental  SLSYMVGMIASFYDTETVIMAVGITAVVCFTVVLFSLQSKYDFTSCRGVLFVCLIVLLLFAFLCIFIRHR
          SLSYMVGMIASFYDTETVIMAVGITAVVCFTVVLFSLQSKYDFTSCRG.LFVCLIVLLLFAFLCIFIRHR
Retrocopy SLSYMVGMIASFYDTETVIMAVGITAVVCFTVVLFSLQSKYDFTSCRGELFVCLIVLLLFAFLCIFIRHR

Parental  ILHIVYASLGALLFTCFLAVDTQLLLGNKKLALSPEEYIFAALNLYT
          ILHI.YASLGAL.FTCFLAVDT.LLLGNKKLALSPEEY.FA.....T
Retrocopy ILHIAYASLGALRFTCFLAVDTPLLLGNKKLALSPEEYVFASTSTLT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_15 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_15 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000005238	1 retrocopy	retro_gacu_15 ,