RetrogeneDB ID: retro_ecab_656

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 26:17978559..17979363(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPA2
• Ensembl ID: ENSECAG00000006379
• Aliases: None
• Description: non imprinted in Prader-Willi/Angelman syndrome 2 [Source:HGNC Symbol;Acc:17044]

Sequence

>retro_ecab_656
GAGATGGCCAACTTTACTGTTTATGTTTACAATGGCAAGACTAGTGACTTAGAAGTTTTTCATGTTCTAGTAAGTGCTAT
TTTTCTTCATATTTTCTAAACAAAAGACTAAATTTTCATGGGAAAATTGAGTGCTTGTTAAACTGCCCTCAATCTCCACT
TACAGTCATTCATGCTTCAAAAGAAGAGAAGTTAGAGACTAACAAAATGTCTCACAAGCTAATTGATCTGGGTTTGGGGT
TTTTGAAGTCTTTGTGGTCATTGTGTCGTCTGTGGTAGGATCTTGCTCTAGACAGACCAACATTTATATAACAATATGCT
CCGTAATTAAAGCATTTTCTGTATCCTGTTTTAAAGGCTTGGATATTGTTATTAAATAACTTCTTGTGGGAAAGTCTCTT
CTGGACATCCCTTGGCTCATTCTTCTGCTGAGTTTTATAGTCTGTGTAAGCACACAGATTAATTATCCAAATAGGCCCTA
GATATAATCAACACTTCTACAGTGACTCCGTTATGTTAGGTATTCTTTGAAGCATCAGTTTTGACTAGTTCAGTTCTTCT
TTGAAAGGAGTGACAAGATATGTCTGCTGATAGTACTTTGAGCTCCTCCTTTACAATTTTGTTGGAAAAAATTTTGTAAT
ATTTTTGTGCCTTTAAAGACCTCAGTTTTCATCTACCAAGCCAGCCTATGTCCTTTCAAAAAGATGAAAAAGTAACGAAT
GACAATCACTGTAATACGTATGTATTTCTTAATAATAATGAAAAAAACTTAACTGGTGTAATTAAACAGCAAACTGAAGA
AAAT

Alignment

ORF - retro_ecab_656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.89 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVANFAAYAFAPATLVTPLGALSVLVSAIL-SSYFLNERLNLHGKIGCLLSILGSTVMVIHAPKEEEIET
          E.ANF..Y.....T....L....VLVSAI..SSYFLN.RLN.HGKI.CLL....S...VIHA.KEE..ET
Retrocopy EMANFTVYVYNGKT--SDLEVFHVLVSAIF<SSYFLNKRLNFHGKIECLLNCPQSPLTVIHASKEEKLET

Parental  LNEMSHKLGD-PGFVVFATLVVIVSLILIFVVGPRHGQTNILVYITICSVIGAFSVSCVKGLGIAIKELF
          .N.MSHKL.D..GF.VF...VVIVS......VG....QTNI..YITICSVI.AFSVSC.KGL.I.IK.L.
Retrocopy -NKMSHKLID<SGFGVFEVFVVIVSSV----VGSCSRQTNI--YITICSVIKAFSVSCFKGLDIVIK*LL

Parental  AGKPVLRHPLAWILLLSLIVCVSTQINYLNR-ALDIFNTSIVTPIYYVFFTTSVLTCSAILFKEWQDMPV
          .GK..L..P...ILLLS.IVCVSTQINY.NR.ALDI.NTS.VTP...VFF..SVLT.S..L.KE.QDM..
Retrocopy VGKSLLDIPWL-ILLLSFIVCVSTQINYPNR<ALDIINTSTVTPLC*VFFEASVLTSSVLL*KE*QDMSA

Parental  DDVIGTLSGFFTIIVGIFLLH--AFKDVSFSLASLPVSLRKDEKAVNGNLSNMYEVLNNNEESLTCGIEQ
          D....TLS..FTI.....L....AFKD.SF.L.S.P.S..KDEK..N.N..N.Y..LNNNE..LT..I.Q
Retrocopy D---STLSSSFTILLEKIL*YFCAFKDLSFHLPSQPMSFQKDEKVTNDNHCNTYVFLNNNEKNLTGVIKQ

Parental  HTSEN
          .T.EN
Retrocopy QTEEN

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.00 RPM	12.57 RPM
SRP021940_cerebellum	0.00 RPM	31.52 RPM
SRP021940_embryo	0.00 RPM	23.68 RPM
SRP021940_placental_villous	0.00 RPM	25.11 RPM
SRP021940_synovial_membrane	0.00 RPM	17.87 RPM
SRP021940_testis	0.00 RPM	41.63 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_656 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_656 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_656 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656 ,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581, retro_ocun_773, retro_ocun_809,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347, retro_itri_388,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285,