RetrogeneDB ID: retro_mgal_17

Retrocopy location

• Organism: Turkey (Meleagris gallopavo)
• Coordinates: Z:5196288..5196843(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PLEKHB2
• Ensembl ID: ENSMGAG00000001052
• Aliases: None
• Description: None

Sequence

>retro_mgal_17
CAGAATTGCCATGATATAGAAGATAAAATCCACATGAGAATCTATTGCATCAACCTCAGAGTGGGGAATGAATATTGAGA
TTTCCAGCCTCCGGAAGGAAAGCAGAGAGACTGTTCACTGCAGATTGTTTGTTGGGATGGTAAGATCATCAACCTCTGTG
CAGAAAGTGCAGATGACTGTTTGGCATAAAACACTGCTCTTCAGGATGCCAGAACAAACATAAGCTACGTGATATCTGAT
GTATGATGAGACAGCAATTTCCTCAACCTCTCCTCCTCATACAGCTTATGCTACACCATCACCTGAAATCTATGGTTATG
GCTATGGTCAGTACAATGTTGCATATCCCACCATGGGTCCTCAGGTCTTCTATGCCCCACTGGACAATCCTATGATGTTC
CCTACCTGTATCCGTACCACAGACCATATGACCAACCCCCTGCAAACCATGTCATCATTTGAGAGCGTTACTGCAAGAGT
GAAGGAGATCTTGCACTGGACATGCTTGCTGAAGCAGTGACTAGAATGGCTCTGGGATTGTTATTCTGGGTCTTC

Alignment

ORF - retro_mgal_17 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.37 %
• Parental protein coverage: 83.18 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QNRHDIEDKIHMRIHCINLRVGNECQDFQPPEGKQRDCLLQIVCRDGKTINLCAESADDCLAWKIALQDA
          QN.HDIEDKIHMRI.CINLRVGNE..DFQPPEGKQRDC.LQIVC.DGK.INLCAESADDCLA...ALQDA
Retrocopy QNCHDIEDKIHMRIYCINLRVGNEY*DFQPPEGKQRDCSLQIVCWDGKIINLCAESADDCLA*NTALQDA

Parental  RTNTGYVGSDVMYDETAI-SSAPPPYTAYATPSPEVYGYGYGQYHGAYPTVGPHVFYA-SNGQAYQ----
          RTN..YV.SDV..D......S.P....A...P..E.YGYGYGQY..AYPT.GP.VFYA...GQ.Y.....
Retrocopy RTNISYVISDV**DSNFL>TSPPHTAYATPSP--EIYGYGYGQYNVAYPTMGPQVFYA<PTGQSYDVPYL

Parental  YPYHGPYGQPPANHVIIRERYRDSDGDLALGMLAGAATGMALGSLFWVF
          YPYH.PY.QPPANHVII.ERY..S.GDLAL.MLA.A.T.MALG.LFWVF
Retrocopy YPYHRPYDQPPANHVII*ERYCKSEGDLALDMLAEAVTRMALGLLFWVF

Legend:

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

Expression

RNA-Seq

Meleagris gallopavo was not studied using RNA-Seq expression data.

ChIP-Seq

Meleagris gallopavo was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mgal_17 retrocopy.

TSS

Meleagris gallopavo was not studied using FANTOM5 data.

Lab

retro_mgal_17 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mgal_17 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000941	2 retrocopies	retro_btau_1134, retro_btau_1635,
Cavia porcellus	ENSCPOG00000026329	1 retrocopy	retro_cpor_985,
Equus caballus	ENSECAG00000017331	1 retrocopy	retro_ecab_1069,
Felis catus	ENSFCAG00000027063	1 retrocopy	retro_fcat_213,
Homo sapiens	ENSG00000115762	1 retrocopy	retro_hsap_1890,
Meleagris gallopavo	ENSMGAG00000001052	1 retrocopy	retro_mgal_17 ,
Monodelphis domestica	ENSMODG00000018634	1 retrocopy	retro_mdom_720,
Nomascus leucogenys	ENSNLEG00000010698	2 retrocopies	retro_nleu_1471, retro_nleu_2016,
Oryctolagus cuniculus	ENSOCUG00000024282	1 retrocopy	retro_ocun_654,
Otolemur garnettii	ENSOGAG00000028408	2 retrocopies	retro_ogar_2771, retro_ogar_703,
Pongo abelii	ENSPPYG00000012740	1 retrocopy	retro_pabe_1570,
Ictidomys tridecemlineatus	ENSSTOG00000020509	1 retrocopy	retro_itri_56,