RetrogeneDB ID: retro_meug_1988

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold77183:1136..1823(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBP2
• Ensembl ID: ENSMEUG00000001887
• Aliases: None
• Description: poly(rC) binding protein 2 [Source:HGNC Symbol;Acc:8648]

Sequence

>retro_meug_1988
GAGATGTTACCAAACTCAACTGAGTAGACCATCATAGTTGCTGGCATCTCGCAATCTATCATTGAGTGTGTCAAACAGAT
CTGTGTGGTCATGTTAGAGCCTCTCTCCCAGTCTCCCCCAAATGGTGTGACCATCCCTTACTGGCCCAAGCCATCCAGCT
CTCCAGTCATTTTTGTAGGTGGTCAGGACAGGTACAGAACAGGCAGCAACAGTGTGAGCTTTCCTCACACCACCATGGCC
TTGTGCCTCAACTCTGACCTGGAGGGGCCACCTCTAGAGGGCTATACCATTCAAGGACAGTATGCCCTTCCACAGCTGGA
TTTGACCAAGCTGAACCAGTTGATAATGCAAGAGTCTCACTTTCCCATTACACATGGCAACACAGGATTCAGTGGCTTTG
AATTCAGCTCTTCATAGGTGAAAGTCTGTTGGAGTTTGGATCTATCTGCTCAAACTACTTCTCTTGAACTCGCCATTCCA
AATAACTTAATTGGCTGCATAATGGGGTTTTAAGGCTCCAGAATCAATGAGATTAGTTGTCAGATGTCTGGGGTTCAGAT
CGAAAATCACCGATTCAGCAGATCTACTGATAGGCAGGTTATCATAACTGGATCCGCTGCCAGCATTATCCTGGCCCAAT
ATCTAACCAATGTCAGATTTTCCTTGGAGACAGGTGGTATGGGGAGC

Alignment

ORF - retro_meug_1988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 62.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DMLPNSTERAITIAGIPQSIIECVKQICVVMLETLSQSPPKGVTIPYRPKPSSSPVIFAGGQDRYSTGSD
          .MLPNSTE..I..AGI.QSIIECVKQICVVMLE.LSQSPP.GVTIPY.PKPSSSPVIF.GGQDRY.TGS.
Retrocopy EMLPNSTE*TIIVAGISQSIIECVKQICVVMLEPLSQSPPNGVTIPYWPKPSSSPVIFVGGQDRYRTGSN

Parental  SASFPHTTPSMCLNPDLEGPPLEAYTIQGQYAIPQPDLTKLHQLAMQQSHFPMTHGNTGFSGSEPRVPKV
          S.SFPHTT...CLN.DLEGPPLE.YTIQGQYA.PQ.DLTKL.QL.MQ.SHFP.THGNTGFSG.E.....V
Retrocopy SVSFPHTTMALCLNSDLEGPPLEGYTIQGQYALPQLDLTKLNQLIMQESHFPITHGNTGFSGFEFSSS*V

Parental  KGYXXGLDASAQTTSHELTIPNDXXXXXXXXQGAKINEIR-QMSGAQIKIANPVEGSTDRQVTITGSAAS
          K.....LD.SAQTTS.EL.IPN..........G..INEI..QMSG.QI........STDRQV.ITGSAAS
Retrocopy K-VCWSLDLSAQTTSLELAIPNNLIGCIMGF*GSRINEISCQMSGVQIE-NHRFSRSTDRQVIITGSAAS

Parental  ISLAQYLINVRLSSETGGMGS
          I.LAQYL.NVR.S.ETGGMGS
Retrocopy IILAQYLTNVRFSLETGGMGS

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1988 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1988 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 19 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020757	1 retrocopy	retro_btau_175,
Canis familiaris	ENSCAFG00000006821	1 retrocopy	retro_cfam_54,
Callithrix jacchus	ENSCJAG00000018590	2 retrocopies	retro_cjac_3253, retro_cjac_754,
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193, retro_cpor_97,
Equus caballus	ENSECAG00000022389	1 retrocopy	retro_ecab_67,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83,
Gorilla gorilla	ENSGGOG00000012613	2 retrocopies	retro_ggor_212, retro_ggor_2734,
Macropus eugenii	ENSMEUG00000001887	7 retrocopies	retro_meug_1143, retro_meug_1988 , retro_meug_432, retro_meug_526, retro_meug_618, retro_meug_828, retro_meug_964,
Macropus eugenii	ENSMEUG00000006975	3 retrocopies	retro_meug_271, retro_meug_357, retro_meug_484,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus	ENSMLUG00000009971	3 retrocopies	retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Mus musculus	ENSMUSG00000056851	1 retrocopy	retro_mmus_274,
Nomascus leucogenys	ENSNLEG00000017693	1 retrocopy	retro_nleu_10,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Pongo abelii	ENSPPYG00000004581	2 retrocopies	retro_pabe_3346, retro_pabe_92,
Pan troglodytes	ENSPTRG00000005018	1 retrocopy	retro_ptro_113,
Rattus norvegicus	ENSRNOG00000036852	2 retrocopies	retro_rnor_1238, retro_rnor_2088,
Sus scrofa	ENSSSCG00000000274	1 retrocopy	retro_sscr_61,