RetrogeneDB ID: retro_zmay_13

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 1:278100262..278101642(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G328224
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G031138
• Aliases: None
• Description: None

Sequence

>retro_zmay_13
ATGGTCATGGCGGCACCTCGTGTTCTAGTTCTGCCTTACCCCGCCCAGGGCCATGTCATCCCTATGATGGAGCTCTCCCA
CTGCCTCATCGAGCACGGCGTCAAGGTCACCTTCGTCAACACCGAGGTAAACCACCGTCTCATTCTTGGTGCCTTGGCGA
CCGGAGACAAAGAACTCGGCGGGGTCGACATGGTGTCCATACCGGACGGCCTGGGCACCGGCGAAGACCGGAAGGACCTC
GGCCGTCTCACCGACTCGTTCTCCAAGGTCATGCCCGGCGAGCTGGAGAAGCTCATTACAAGCATCAACGCCGATGGACG
AGAGCGCGAGAAGGTCAGCTGGTTGATCGCCGACGTGAACATGGCGTGGGCCTTCCCTGTGGCGAAGAAGCACGGCCTCC
GAACCGCCGGGTTCTGCCCATCGTCGGCGGCGATGTTCGCGATGAGGATCAGAATTCCTGAGATGATAAGCGACGGCGTT
CTTGACGAGAGAGGCTGGCCCAAGCGGCGCGGCGCGTTCCAGTTGGCTCCGGCGATGCCGGCCATCGACACTTCGGAGTT
CTCGTGGAACCGTGCCGCCGACGCCAAGGGGAAGCCGATCATCTTTCAGCTGATCCTCCGGAACAACGCGGCCACGCACC
TCGCCGAGACCATCGTCTGCAACTCCATCCAAGAGCTGGAGCCCGGAGCCTTGGCGCTCGTCCCCGACGTCTTCCCCGTG
GGCCCGCTCTCCTCCGACAAACCGGTCGGCTGCTTCTGGGCCGAAGACGCCTCCTGCCCCGCGTGGCTGGACGCGCAGCC
GGCCAGCTCCGTCGTGTACGTCGCGTTCGGCAGCCTCGCCGCCTACGGCGCCGCGCAGCTAGTCGAGCTGGCCGAGGGGC
TGCTGCTGACCTCCCGGCCGTTCCTGTGGGTGGTCAGGCCGGGGTCGACGGGCGAGCAGCACCTTGAGCAGCTCCGCCGC
CGCGCCGCGCCGCGCGGGCGCGTGGTGAGCTGGTGCCCGCAGCAGAACGTGCTGGCGCACCACGCGGTCGCCTGCTTCCT
GACGCACTGCGGCTGGAACTCGACGATGGAGGCGGTGCGGAACGGCGTGCCCCTCCTGTGCTGGCCGTATTTCACCGACC
AGTTTCTGAACCAGAGCTACATCTGCGACGTGTGGAGGACGGGACTGAAGGTTCCATTGCCGCCAGGGGCGGCGCACGGA
ACGGGACTCGTGGGGAGAGACGTTGTTCGGGACAAGATCGAGGAGCTGCTCCGTGACAGTGAGACGAAGGCGAGGGCGCT
CGCGCTGCGGGACCTCGCCAGTCGGGCAGTCGGCGATGGAGGTTCGTCGCGCCGGAATCTCAGGCAGTTCTTGGGCCTTG
TGCGAGGATCGGAGAGCTAA

Alignment

ORF - retro_zmay_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.3 %
• Parental protein coverage: 85.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLVLPMPCQGHVTPLMELSHLLVDQGFEVTFVNTDVDRAAVVAALEASGGVAALGGGIHLASIPDGLADD
          VLVLP.P.QGHV.P.MELSH.L...G..VTFVNT.V.......AL....G...LG.G....SIPDGL...
Retrocopy VLVLPYPAQGHVIPMMELSHCLIEHGVKVTFVNTEVNHRLILGAL--ATGDKELG-GVDMVSIPDGLGTG

Parental  EDRKDISKLVDAYTRHMPGYLERLLADMEAAGRPRAK--WLVADTNMGWSFEVAKKLGIRVVSFWPAATA
          EDRKD...L.D.....MPG.LE.L.....A.GR.R.K..WL.AD.NM.W.F.VAKK.G.R...F.P...A
Retrocopy EDRKDLGRLTDSFSKVMPGELEKLITSINADGREREKVSWLIADVNMAWAFPVAKKHGLRTAGFCPSSAA

Parental  CLAFMLKIPKLIQDGLLDDKGLPVRQETFQLAPGMPPLHSSQLSWNNAGEPEGQHIIFELVTRNNKLNDE
          ..A....IP..I.DG.LD..G.P.R...FQLAP.MP....S..SWN.A....G..IIF.L..RNN.....
Retrocopy MFAMRIRIPEMISDGVLDERGWPKRRGAFQLAPAMPAIDTSEFSWNRAADAKGKPIIFQLILRNNAAT-H

Parental  LAEMVVSNSFYEAEAGAFKLFPGILPIGPLSADGAFRKPVGHYLPEDERCVKWLDAHPDASSVVYVAFGS
          LAE..V.NS..E.E.GA..L.P...P.GPLS.D....KPVG....ED..C..WLDA.P.ASSVVYVAFGS
Retrocopy LAETIVCNSIQELEPGALALVPDVFPVGPLSSD----KPVGCFWAEDASCPAWLDAQP-ASSVVYVAFGS

Parental  ITIFSARQFEELAEGLELTGRPFLWVVRPDFTPGLSKAWLHEFQRRVAGRGMIVSWCSQQQVLAHRAVAC
          .....A.Q..ELAEGL.LT.RPFLWVVRP..T.......L....RR.A.RG..VSWC.QQ.VLAH.AVAC
Retrocopy LAAYGAAQLVELAEGLLLTSRPFLWVVRPGST---GEQHLEQLRRRAAPRGRVVSWCPQQNVLAHHAVAC

Parental  FVSHCGWNSTMEGLRNGVPFLCWPYFCDQYLNRSYIVNVWRTGLAV
          F..HCGWNSTME..RNGVP.LCWPYF.DQ.LN.SYI..VWRTGL.V
Retrocopy FLTHCGWNSTMEAVRNGVPLLCWPYFTDQFLNQSYICDVWRTGLKV

Legend:

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

Expression

RNA-Seq

Zea mays was not studied using RNA-Seq expression data.

ChIP-Seq

Zea mays was not studied using ChIP-Seq data.

EST

Zea mays was not studied using EST data.

TSS

Zea mays was not studied using FANTOM5 data.

Lab

retro_zmay_13 was not experimentally validated.

Homology

Retrocopy orthology:

Zea mays does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G031138	1 retrocopy	retro_zmay_13 ,
Sorghum bicolor	Sb01g007640	1 retrocopy	retro_sbic_14,