RetrogeneDB ID: retro_hsap_2521

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 21:30275407..30276112(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000215317
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: THUMPD1
• Ensembl ID: ENSG00000066654
• Aliases: None
• Description: THUMP domain containing 1 [Source:HGNC Symbol;Acc:23807]

Sequence

>retro_hsap_2521
TCACACCCGTAAACCGTGGAGAAGTTCGCCGGGAGGTGAGGACGCCAACTGCAGTGGAGAAACGTTTCTCTTTCCTCTCA
GCTTGCACACATCATGGCGGCTGCTGCCCAGCAGCCTCCTCAGCCTGGCGGCGGGAAGCACAGAGGCAAGGCTCAGTATG
TGCTGGTCAAGCGAGCTCGGCACTGCGAATCTGGCGGGCCCAGTCAGCCAGAGCCCGGGCTACGGGCATCCTCATCACCT
GCAACATGAACCAGCGCCAAGTGTGTGGAGGAGGCTTACACCCTGCTCAACGAATATGGCGATGACATGTATGGGCCAGA
AAAGTTTACAGACAAGGATCAGCAGCCCTCTGGAAGTGAGGGAGAAGATGATGATGTGGAGGCTGTCTTGAAGAAAGAAG
TTGGTGACATTGAGGCATCTACAGAGATGAGCCTAAGAGGATTCCAGTCAGTGGAAAGTGGAGCAAATAACGTCGCCTTC
ATCAGGACACTTGGGAAAGAACCTGAGAAACTGGTGCATCATATTCTCCAGGATGAGTACAAAACCAAGAAGACTCAAGT
TATTCTACGAATGTTACCCATCTCAGGCACATGCAAAGCTTTTTTAAAAGATATGAAAAAATATGCAGAAACATTTTTGG
AACCCTGGTTTAAAGCTCCAAACAAAGGGACATTTCAGATTGTGTACAAATCTTGAAATAGCAGT

Alignment

ORF - retro_hsap_2521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.59 %
• Parental protein coverage: 53.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SYPTSPVRAGDRRGRQQQRRNVSLSSQFAHTMAAPAQQTTQPGGGKRKGKAQYVLAKRARRCDAGGPRQL
          S.P........R.GRQ.Q.RNVSLSSQ.AH.MAA.AQQ..QPGGGK..GKAQYVL.KRAR.C..GGP.Q.
Retrocopy SHP*TVEKFAGR*GRQLQWRNVSLSSQLAHIMAAAAQQPPQPGGGKHRGKAQYVLVKRARHCESGGPSQP

Parental  EPGLQ-GILITCNMNER-KCVEEAYSLLNEYGDDMYGPEKFTDKDQQPSGSEGEDDDAEAALKKEVGDIK
          EPGL..GILITCNMN.R.KCVEEAY.LLNEYGDDMYGPEKFTDKDQQPSGSEGEDDD.EA.LKKEVGDI.
Retrocopy EPGLR<GILITCNMNQR>KCVEEAYTLLNEYGDDMYGPEKFTDKDQQPSGSEGEDDDVEAVLKKEVGDIE

Parental  ASTEMRLRRFQSVESGANNVVFIRTLGIEPEKLVHHILQDMYKTKKKKTRVILRMLPISGTCKAFLEDMK
          ASTEM.LR.FQSVESGANNV.FIRTLG.EPEKLVHHILQD.YKT..KKT.VILRMLPISGTCKAFL.DMK
Retrocopy ASTEMSLRGFQSVESGANNVAFIRTLGKEPEKLVHHILQDEYKT--KKTQVILRMLPISGTCKAFLKDMK

Parental  KYAETFLEPWFKAPNKGTFQIVYKSRNNS
          KYAETFLEPWFKAPNKGTFQIVYKS.N.S
Retrocopy KYAETFLEPWFKAPNKGTFQIVYKS*NSS

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
bodymap2_adipose	0.00 RPM	46.91 RPM
bodymap2_adrenal	0.00 RPM	63.97 RPM
bodymap2_brain	0.00 RPM	43.48 RPM
bodymap2_breast	0.00 RPM	59.24 RPM
bodymap2_colon	0.00 RPM	65.10 RPM
bodymap2_heart	0.00 RPM	30.66 RPM
bodymap2_kidney	0.00 RPM	84.58 RPM
bodymap2_liver	0.00 RPM	22.37 RPM
bodymap2_lung	0.07 RPM	41.63 RPM
bodymap2_lymph_node	0.00 RPM	52.34 RPM
bodymap2_ovary	0.00 RPM	101.67 RPM
bodymap2_prostate	0.00 RPM	89.08 RPM
bodymap2_skeletal_muscle	0.00 RPM	27.66 RPM
bodymap2_testis	0.00 RPM	81.41 RPM
bodymap2_thyroid	0.00 RPM	80.64 RPM
bodymap2_white_blood_cells	0.00 RPM	86.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2521 was not detected

EST

No EST(s) were mapped for retro_hsap_2521 retrocopy.

TSS

No TSS is located nearby retro_hsap_2521 retrocopy 5' end.

Lab

retro_hsap_2521 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2521 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1466
Gorilla gorilla	retro_ggor_1573
Macaca mulatta	retro_mmul_1599

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009499	1 retrocopy	retro_cjac_915,
Cavia porcellus	ENSCPOG00000008919	1 retrocopy	retro_cpor_71,
Felis catus	ENSFCAG00000015158	1 retrocopy	retro_fcat_195,
Homo sapiens	ENSG00000066654	1 retrocopy	retro_hsap_2521 ,
Gorilla gorilla	ENSGGOG00000005231	1 retrocopy	retro_ggor_1573,
Macaca mulatta	ENSMMUG00000004225	1 retrocopy	retro_mmul_1599,
Monodelphis domestica	ENSMODG00000006971	1 retrocopy	retro_mdom_54,
Nomascus leucogenys	ENSNLEG00000012369	1 retrocopy	retro_nleu_1443,
Pan troglodytes	ENSPTRG00000007848	1 retrocopy	retro_ptro_1466,